Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,542	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,542	0	C	A	100.0%	159.7 / NA	56	P1100Q (CCG→CAG)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (25/31);  total (25/31)

TAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAG  >  NC_000913/4184411‑4184681                                                                                                                                    |                                                                                                                                            tcaaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCAGGGTAACAAGGGTGTCATTTCTAAGAGCATCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAc                                                                                                                                  <  1:658887/141‑1 (MQ=255)  aaaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAcc                                                                                                                                 >  2:113670/1‑143 (MQ=255)  aaaCGCCGTATCCAGCCTGGAGACAAGATGGCAGGTAGTCACGGTAACAAGGATGTAAACAACAGGTTCTAGCCGAGCGAAGATATGCCTTCCGATGAAAACGCTACGCCGGTAGACATCGACCTGCACCAGCTGGGCggccc                                                                                                                                 >  1:394645/1‑139 (MQ=255)    aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACACGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGCTAGACATCGGACTGAACCAGCTGGGCGCAccct                                                                                                                               >  1:261088/1‑141 (MQ=255)       ccGTCTCGAGTCTGGTGACAAGATGGCAGGTCGGCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGAACTGtctc                                                                                                                            <  1:661050/143‑1 (MQ=255)       ccGTATGCAGCCGTGTGACAAGATGGCAGGTCGTCGCGGTAGCGTGGGTGTAATTTCTAAGATCAACCCGATAGACGATATGCCTTACGATGAAGACGGTACGCCGGTAGTTTTCGTGCTGAACCAGCTGGGCGTACCGtctc                                                                                                                            <  1:304817/143‑1 (MQ=255)       ccGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                            >  2:576114/1‑143 (MQ=255)         gTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                          <  1:669387/143‑1 (MQ=255)          tATCCAGCCTGGTGACATGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                         <  1:517070/143‑1 (MQ=255)           aTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGCAACCGCGCCGGCGGTATTCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                        <  2:188558/143‑1 (MQ=255)           aTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                        <  2:77424/143‑1 (MQ=255)                   tGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCACATCg                                                                                                                >  2:882163/1‑143 (MQ=255)                   tGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                                >  2:922051/1‑143 (MQ=255)                       gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAGCATCGGGCa                                                                                                            >  2:593235/1‑143 (MQ=255)                        aCAAGATGGCAGGTCGTCACGGTAACAAGGATGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAg                                                                                                           >  2:554335/1‑143 (MQ=255)                         cAAGATGGCAGGCCGTCACGGCAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGa                                                                                                          <  2:753494/143‑1 (MQ=255)                          gaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCAAATCGGTCAGAt                                                                                                         >  1:867667/2‑143 (MQ=255)                          aaGATGGCAGGTCGTCACGGTAACAAGGGTGTACACTTAGTTTTTAATCCGATCGAAGATATGCCCTACGGGTATATCGGTTTGCCGGGAGACATCGTACGGAACCAGCTGGGCGGGGCGTCGCGTGTTAAGAGCGGTCGGAt                                                                                                         >  1:599151/1‑143 (MQ=255)                          aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                                         >  1:415000/1‑143 (MQ=255)                            gctGGCAGGTCGGCACGGTAACAAGGGTGTAATTTCTAAGATCATACCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGATCCAGCTGGGCGTACTGTCTCGTATGAACATCGGTCAGATcc                                                                                                       <  1:778702/141‑1 (MQ=255)                              tGGCGGGTCGTCACGGTAACAAGGGTGTAAGTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                     <  2:823735/143‑1 (MQ=255)                                gCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGa                                                                                                   >  2:620688/1‑143 (MQ=255)                                gCAGGTCGCCACCGTAACAAACGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGa                                                                                                   <  2:273235/143‑1 (MQ=255)                                 cAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaa                                                                                                  >  1:231309/1‑143 (MQ=255)                                  cggTCGTCACGGTAACAAGGGTGTAATGTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                 <  1:143463/142‑1 (MQ=255)                                  aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATGAACCCGATCGAAGAGATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                 <  1:768005/143‑1 (MQ=255)                                    gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGAGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAcc                                                                                               <  1:866897/143‑1 (MQ=255)                                     tcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCCGCGCCGCGAAAccc                                                                                              >  1:127631/1‑143 (MQ=255)                                       gtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTGCGCCGGTAGACATCGTACTGGACCAGCTGGCCGTACCGTCTCGTATAAACATCGGGCAGATCGTCGAAAgccgc                                                                                            >  2:236493/1‑141 (MQ=255)                                          aCGGTAACAAGTGTGTAATTTCTAAGCTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGCACCGCCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTg                                                                                         <  1:624708/143‑1 (MQ=255)                                          aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAACTg                                                                                         >  2:294501/1‑143 (MQ=255)                                                  aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACCTCGGTCAGATCCTCGAAACCCACCCGGGTATGGc                                                                                 >  1:46227/1‑143 (MQ=255)                                                     ggTGTACTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                              <  1:481798/143‑1 (MQ=255)                                                         tattttCTAAGTTCAACCCGATCGCAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                          <  2:40168/140‑1 (MQ=255)                                                         tagcttCTAAGATCAACCCGATCGAAGATATGCCCGCCGATGAAAACGGCACGCCGGTCGCCATCGTACTGAACCAGCCGGGCGCACCGTCGCGTATGAACATCGGTCAGCTCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                          <  1:515638/139‑1 (MQ=255)                                                         tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                          <  2:86434/143‑1 (MQ=255)                                                         tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTCGGTATGGCTGCGaaa                                                                          >  1:781746/1‑143 (MQ=255)                                                               gcacgATCAATCCGATCGAAGATATGCCGTACGATGAAGACGGTACGCGGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCGCGTATGAACATCGGTCAGAGCCTCGAATCCCACCTTGGTATGGCTGCGAAAGGTATc                                                                    <  1:371545/139‑1 (MQ=255)                                                               cTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGGACTGAACCAGCTGGGCGTACCGTCACGTATGAACATCGGACAGATCCTCGAAACCCACCGGGGGATGGCTGCGAAAgggagc                                                                    >  1:191265/1‑139 (MQ=255)                                                                tAAGATCAAGCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTTGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                                   <  1:392981/143‑1 (MQ=255)                                                                         cccgcgcggaGATATGCCTTACGATGTGAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTCTGAACATCGGTCAGATCCACGAACCACAACTTGTTATGGCTGCGAAGGGTTTCGGCGACAAGa                                                          <  1:19100/134‑1 (MQ=255)                                                                         cccGATCGACGAGATCGCTGGTGATGCAAACGGGACGCCGGTTGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATAGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                          <  1:469735/143‑1 (MQ=255)                                                                         cccGATCGAAGATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                          <  2:127331/143‑1 (MQ=255)                                                                          ccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAGACCCACATGGGTATGGCGGAGAAAGGTATCGGCGACCAGAt                                                         >  1:705739/1‑143 (MQ=255)                                                                          ccGAGCGAAGATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAt                                                         <  1:761063/143‑1 (MQ=255)                                                                                gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATACTCGAAACCCACCTGGGTATGGCTGCGACACGGATCGACGACAAGATCAACGc                                                   >  1:871459/1‑143 (MQ=255)                                                                                                aTGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcagcag                                   >  2:543954/1‑143 (MQ=255)                                                                                                 tGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACagcagc                                  <  2:645847/143‑1 (MQ=255)                                                                                                      aCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaagaa                             <  2:599151/143‑1 (MQ=255)                                                                                                             gCCGTTAGTCACCGTACTGAACCATCTCTGCTTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                      <  1:328231/143‑1 (MQ=255)                                                                                                                     aCATCGTACTGAACCAGCTGGGCGTACCGACTCGTATGAACACCGGTCAGAGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc              <  2:521575/143‑1 (MQ=255)                                                                                                                      cATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGcgcg             >  2:575311/1‑143 (MQ=255)                                                                                                                       aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGa            >  1:975440/1‑143 (MQ=255)                                                                                                                         cGTACTGAGCCAGCTGGGCGTACAGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAAt          <  1:781108/143‑1 (MQ=255)                                                                                                                                 aCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAg  >  2:568247/1‑143 (MQ=255)                                                                                                                                 aCCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAg  <  2:249717/143‑1 (MQ=255)                                                                                                                                    |                                                                                                                                            TAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCAG  >  NC_000913/4184411‑4184681

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑