BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	9,710	T→C	7.3%	intergenic (+15/+72)	gyrA → / ← nnrD	DNA gyrase subunit A/ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	9,710	0	T	C	7.3%	452.8 / 19.8	164	intergenic (+15/+72)	gyrA/nnrD	DNA gyrase subunit A/ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase
Reads supporting (aligned to +/- strand): ref base T (72/78); new base C (4/8); total (77/87)
Fisher's exact test for biased strand distribution p-value = 3.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.29e-01

Only 100 of 167 total aligned reads displayed.

AATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATACAT  >  USA300TCH1516_ALE/9573‑9850

  tGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCta                                                                                                                                          <  2:297164/141‑1 (MQ=255)

    cAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCtata                                                                                                                                        <  2:186298/141‑1 (MQ=255)

    cAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCtaca                                                                                                                                        <  2:338472/141‑3 (MQ=255)

    cAATGCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCtata                                                                                                                                        <  2:552855/141‑1 (MQ=255)

     aaTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTatat                                                                                                                                       >  1:653850/1‑141 (MQ=255)

     aaTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTatat                                                                                                                                       >  1:688030/1‑141 (MQ=255)

      aTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCtacata                                                                                                                                      <  3:370566/141‑5 (MQ=255)

       ttCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGt                                                                                                                                     <  2:476128/141‑1 (MQ=255)

           tACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAggg                                                                                                                                 >  4:351158/1‑141 (MQ=255)

            aCTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAgggg                                                                                                                                >  1:997634/1‑141 (MQ=255)

            aCTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAgggg                                                                                                                                <  2:866194/141‑1 (MQ=255)

            aCTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCTACATATAggga                                                                                                                                <  1:113654/141‑2 (MQ=255)

               gAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGt                                                                                                                             <  3:413110/141‑1 (MQ=255)

               gAAGTGAGTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGt                                                                                                                             <  2:224369/141‑1 (MQ=255)

                 aGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCTACATATAGGGAAGTCt                                                                                                                           <  1:432935/141‑1 (MQ=255)

                 aGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCTACATATAGGGAAGTCt                                                                                                                           <  1:433007/141‑1 (MQ=255)

                 aGTGATGGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCTACATATAGGGAAGTCt                                                                                                                           <  2:837236/141‑1 (MQ=255)

                  gTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCtt                                                                                                                          <  1:211969/141‑1 (MQ=255)

                       tgattCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑tttt                                                                                                                    >  3:45603/1‑141 (MQ=255)

                        gattCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑ttttt                                                                                                                   <  2:283433/141‑1 (MQ=255)

                             agaagaAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTCCCCTACATATAGGGAAGTCTTA‑ttttttatta                                                                                                              <  1:618374/141‑6 (MQ=38)

                                  aaaaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCATATATGTCGGGGAGTCTTA‑TTTTTATGCTAGaaa                                                                                                         >  4:349111/1‑141 (MQ=255)

                                    aaTGATGAATGTTGACGTATTCACGGAAGACAACATTTCATCGATCGTTTTTACGATACTCTACAATAATCCGA‑‑‑‑‑‑ACATGAAAAATAAT‑TAACAATAAGACTTCCCTATATGTAGGGGATTCTTA‑TTTTTATGCTCGAAAGt                                                                                                       <  4:167552/141‑1 (MQ=255)

                                    aaTGATGAAGATGGACGTAAGTAATTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGt                                                                                                       <  1:283622/141‑1 (MQ=255)

                                     atgatgAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTa                                                                                                      >  4:27997/1‑141 (MQ=255)

                                      tgatgaAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTaa                                                                                                     <  2:990334/141‑1 (MQ=255)

                                      tgatgaAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTaa                                                                                                     <  4:30878/141‑1 (MQ=255)

                                       gatgaAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAAt                                                                                                    >  4:451077/1‑141 (MQ=255)

                                              aTGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTAc                                                                                             <  1:210719/141‑1 (MQ=255)

                                              aTGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTAc                                                                                             <  2:199616/141‑1 (MQ=255)

                                                ggACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACta                                                                                           >  1:192107/1‑141 (MQ=255)

                                                    gTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATAtt                                                                                       <  4:217761/141‑1 (MQ=255)

                                                     tATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATAAGTAGGGGAGGCTTA‑TTTCTATGCTAGAAAGTAATGCCTTACTATATTc                                                                                      >  2:954296/1‑141 (MQ=255)

                                                        tGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAAt                                                                                   <  2:293606/141‑1 (MQ=255)

                                                            gTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTCTTATGCTAGAAAGTAATGCTTTACTATATTCAATGAtt                                                                               >  2:489259/1‑141 (MQ=255)

                                                             tAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATACTCAATGATTa                                                                              >  2:691956/1‑141 (MQ=255)

                                                               aGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGt                                                                            <  1:564714/141‑1 (MQ=255)

                                                               aGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGt                                                                            >  2:455014/1‑141 (MQ=255)

                                                                gACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTa                                                                           >  1:100784/1‑141 (MQ=255)

                                                                gACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTa                                                                           >  4:335351/1‑141 (MQ=255)

                                                                  cAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGATGAAGAATAATAAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTGTACTATATTCAATGAt                                                                                <  1:451709/141‑1 (MQ=255)

                                                                    aGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGa                                                                       <  2:940476/141‑1 (MQ=255)

                                                                    aGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGa                                                                       >  2:192083/1‑141 (MQ=255)

                                                                    aGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TATTTATGCTAGAAAGTAATGCTTTACTATATTAAATTATTAGTAAGGa                                                                       >  4:190925/1‑141 (MQ=255)

                                                                       tttCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTa                                                                    <  4:444285/141‑1 (MQ=255)

                                                                       tttCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATCACTa                                                                    >  2:788497/1‑141 (MQ=255)

                                                                         tCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAAc                                                                  >  1:232149/1‑141 (MQ=255)

                                                                         tCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAAc                                                                  >  1:134828/1‑141 (MQ=255)

                                                                          cATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACt                                                                 >  3:53366/1‑141 (MQ=255)

                                                                           aTGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACtt                                                                <  3:199929/141‑1 (MQ=255)

                                                                           aTGGATCATGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACGATATTCAATGATTAGTAATGACTAACtt                                                                >  3:402831/1‑141 (MQ=255)

                                                                            tGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACttt                                                               >  3:122668/1‑141 (MQ=255)

                                                                            tGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACttt                                                               >  1:177473/1‑141 (MQ=255)

                                                                              gATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCt                                                             <  3:330685/141‑1 (MQ=255)

                                                                              gATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCt                                                             >  1:1030712/1‑141 (MQ=255)

                                                                              gATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCt                                                             <  2:321510/141‑1 (MQ=255)

                                                                               aTCGTGTTGAAGAAGATATACAACAATCATG‑‑‑‑‑‑AGATGGAGAATAAT‑AAAAAATAAGACTACCCTATATGAAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTa                                                            >  2:913163/1‑141 (MQ=255)

                                                                                  gtgtTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAAtt                                                         <  1:709536/141‑1 (MQ=255)

                                                                                  gtgtTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAAtt                                                         <  1:671668/141‑1 (MQ=255)

                                                                                   tgtTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCNATGATTAGTAATNACTAACTTTCTAATTg                                                        <  1:876416/141‑1 (MQ=255)

                                                                                   tgtTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTg                                                        <  1:111178/141‑1 (MQ=255)

                                                                                    gtTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGt                                                       >  2:457960/1‑141 (MQ=255)

                                                                                      tGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGttt                                                     >  1:489802/1‑141 (MQ=255)

                                                                                       gaagaaGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTc                                                    <  3:180200/141‑1 (MQ=255)

                                                                                         agaagaTATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCAt                                                  >  2:683224/1‑141 (MQ=255)

                                                                                            agaTATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGc                                               >  4:60491/1‑141 (MQ=255)

                                                                                                  acaacaATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAgg                                         <  2:892026/141‑1 (MQ=255)

                                                                                                  acaacaATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAgg                                         <  2:185885/141‑1 (MQ=255)

                                                                                                  acaacaATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAgg                                         <  1:271121/141‑1 (MQ=255)

                                                                                                  acaacaATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAACAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAgg                                         <  1:1041746/141‑1 (MQ=255)

                                                                                                   caacaaTCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGt                                        >  2:393441/1‑141 (MQ=255)

                                                                                                   caacaaTCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGt                                        >  3:272818/1‑141 (MQ=255)

                                                                                                     acaaTCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTAt                                      <  1:833678/141‑1 (MQ=255)

                                                                                                         tcatc‑‑‑‑‑‑aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCa                                  <  2:1026836/141‑1 (MQ=255)

                                                                                                         tcatc‑‑‑‑‑‑aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCa                                  >  2:724733/1‑141 (MQ=255)

                                                                                                         tcatc‑‑‑‑‑‑aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCa                                  >  2:666732/1‑141 (MQ=255)

                                                                                                             c‑‑‑‑‑‑aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGa                              >  2:907586/1‑141 (MQ=255)

                                                                                                             c‑‑‑‑‑‑aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGa                              >  2:736408/1‑141 (MQ=255)

                                                                                                                    acaTGAAGAATAAT‑AAATAATAAGACTTCCCCATATGGAGGGCAGTCTTA‑‑TTTGATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAAGTGTTTCATTGCGTAAGGTATTTCATTGATa                            <  3:327034/139‑1 (MQ=255)

                                                                                                                    aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGAt                             >  2:125287/1‑141 (MQ=255)

                                                                                                                    aGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGAt                             <  1:323896/141‑1 (MQ=255)

                                                                                                                      aTGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATCGATaa                           >  3:68557/1‑141 (MQ=255)

                                                                                                                        gaagaaTAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGt                         >  2:1067252/1‑141 (MQ=255)

                                                                                                                         aagaaTAAT‑AAAAAATAAGACGTCCCTATATGTAGTGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTc                        <  4:415761/141‑1 (MQ=255)

                                                                                                                          agaaTAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGCGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAATTTTCTAATTGTTTCGTTGCGTAAGGTATTTCATTGATGAGTCt                       >  2:548700/1‑141 (MQ=255)

                                                                                                                          agaaTAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCt                       <  2:389844/141‑1 (MQ=255)

                                                                                                                               aat‑aaAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCTTTGCGTAAGGTATTTCATTGATAGGTCTTGAtg                  >  1:682025/1‑141 (MQ=255)

                                                                                                                                at‑aaAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGAtgg                 >  1:728157/1‑141 (MQ=255)

                                                                                                                                    aaaaaTAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGAtggtgg              <  1:94283/141‑1 (MQ=255)

                                                                                                                                       aaTAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGcac           <  3:103367/141‑1 (MQ=255)

                                                                                                                                        aTAAGACTCCCCTACATATAGGGAAGTCTTATTTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGcac           >  1:528655/1‑141 (MQ=38)

                                                                                                                                         tAAGACTCCCCTACATATAGGGAAGTCTTATTTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGcacc          >  3:328910/1‑141 (MQ=38)

                                                                                                                                           aGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCacaaca       >  2:804462/1‑141 (MQ=255)

                                                                                                                                           aGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACcaca       >  1:520281/1‑141 (MQ=255)

                                                                                                                                           aGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACcaca       >  4:14499/1‑141 (MQ=255)

                                                                                                                                           aGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACcaca       >  1:244719/1‑141 (MQ=255)

                                                                                                                                             aCTTCGCTATATATAGGGGAGTCTTA‑TTTTTATGCTATAAAGTAATTCTTTACTATATTTAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacata     <  4:377369/141‑1 (MQ=255)

                                                                                                                                              cTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatac    <  2:635591/141‑1 (MQ=255)

                                                                                                                                                tCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatacat  >  1:698677/1‑141 (MQ=255)

                                                                                                                                                tCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatacat  >  1:815935/1‑141 (MQ=255)

AATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATC‑‑‑‑‑‑AGATGAAGAATAAT‑AAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTA‑TTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATACAT  >  USA300TCH1516_ALE/9573‑9850

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`