Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,420,831 T→C 9.4% Y147C (TAC→TGC)  argT ← lysine/arginine/ornithine transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,420,8310TC 9.4% 108.2 / 3.0 43Y147C (TAC→TGC) argTlysine/arginine/ornithine transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (26/12);  new base C (2/2);  total (28/15)
Fisher's exact test for biased strand distribution p-value = 5.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.45e-01

GCTTGAGGAATCCTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTCGGAGAAGGCAATCTCCTG  >  CP009273/2420691‑2420970
                                                                                                                                              |                                                                                                                                           
gCTTGAGGAATCCTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCATTCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTGACTACGCCAGGTCTCGTTAGCGTAAGCTTcc                                                                                                                                     >  1:266438/1‑149 (MQ=255)
  ttGAGGAATCCTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTCGCGTAAGCTTCCTg                                                                                                                                   >  1:128880/1‑149 (MQ=255)
  ctgcggAATCCTCCGCTGGCTGCAACTTTATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGCCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTg                                                                                                                                   <  1:27701/145‑1 (MQ=255)
       gAATCCTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAACCCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCCCGTTAGCGTAAGCTTCCTg                                                                                                                                   >  2:42738/1‑144 (MQ=255)
          tttctctcTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGt                                                                                                                                >  2:218657/8‑144 (MQ=255)
          tCCTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGt                                                                                                                                >  2:207639/1‑144 (MQ=255)
           ccTGCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGAACAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTTGGtt                                                                                                                               >  2:236505/1‑144 (MQ=255)
            cTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCACACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCCTAAGCTTTCTGGGTTGATccc                                                                                                                         <  1:281532/149‑1 (MQ=255)
             ttCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCt                                                                                                                        >  1:19012/1‑149 (MQ=255)
              tCGCTGGCAGCAACTTCATCTTGTAAGGGATCATCCAGCACTCCATTGAAG‑‑AAAGCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTg                                                                                                                       <  1:287738/149‑1 (MQ=255)
              tCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTg                                                                                                                       <  1:140332/149‑1 (MQ=255)
                  tGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGCAAGCTTCCTGGGTGGATCCCTgcagc                                                                                                                   >  1:361405/1‑149 (MQ=255)
                  tGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCACGTTAGCGCAAGCTTCCTGGGTTGATCCCTgcagc                                                                                                                   >  1:221643/1‑149 (MQ=255)
                   ggCAGCAACTGCATCTTGTAACGCAGCCTCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCGTAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTg                                                                                                                       <  2:196614/144‑1 (MQ=255)
                     cagcaACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATAGGAATAGACCAAATCCTGGTTGGCATAGGCAACAACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAACTTCCTCGGTTGATCCCTgcg                                                                                                                     >  2:303079/1‑143 (MQ=255)
                            ttCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACAt                                                                                                         >  1:59644/1‑149 (MQ=255)
                                   tGTAACGCAGCATCCAGACGTCC‑‑TGTAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTAcc                                                                                                  >  1:199653/1‑149 (MQ=255)
                                            gcaTCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGa                                                                                         >  1:75240/1‑149 (MQ=255)
                                                  agtcGTCC‑‑TGCAGCCAGATCCGAATAGACCCAATCCTGGTTGGCATATGCCACCACATCCGCGCCTTTACTTCGCCAGGTCTCGTTAGCGGAATCTTCCTGGGTTGATCCCTGCAGCACACCAAGATGTTTACCTTTCAGTGaa                                                                                        <  2:51671/141‑1 (MQ=255)
                                                       tCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACACCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAg                                                                                   >  2:237982/1‑144 (MQ=255)
                                                         c‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGc                                                                            >  1:332637/1‑149 (MQ=255)
                                                         c‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGc                                                                            >  1:230422/1‑149 (MQ=255)
                                                             gCAGCCAGAACGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCGTCCTGGGTTGATCCCTGCAGCCCACCAACATGTTTACCTTTCAGTGAGTCCAGCgct                                                                               >  2:183559/1‑142 (MQ=255)
                                                                 ccAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACCCCAACATGTTTCCCTTTCAGTGAATCCAGCGTTGGCAGAATc                                                                      >  1:216521/1‑149 (MQ=255)
                                                                   aGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTgc                                                                         >  2:301999/1‑143 (MQ=255)
                                                                         gAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTCCAGCACACCAACACGTTTACCTTTCAGTGAAACCAGCGTTGGCTGAATCGGt                                                                   >  2:138509/1‑144 (MQ=255)
                                                                            tAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCttt                                                           >  1:316849/1‑149 (MQ=255)
                                                                            caGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTTCTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCttt                                                           <  1:185489/148‑1 (MQ=255)
                                                                               aCCAAATCCTGGTTGGAATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGGTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGc                                                        <  1:201939/149‑1 (MQ=255)
                                                                                  aaaTCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTTAATCCAGCGTTGGCTGAATCTGTGAACCTTTGGCCGc                                                     <  1:252906/149‑1 (MQ=255)
                                                                                  aaaTCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGGCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTAAGTGAATCCAGCGTTGGCTGACTCGGTGCACGTTTGACCGc                                                     >  1:204522/1‑149 (MQ=255)
                                                                                         ggTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCaa                                                   <  2:282582/144‑1 (MQ=255)
                                                                                            tGGCATAGGCCACCACAGCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACga                                           <  1:97773/149‑1 (MQ=255)
                                                                                                      caccacATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTgcgg                                 >  1:354276/1‑149 (MQ=255)
                                                                                                         cacaTCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGt                              <  1:246669/149‑1 (MQ=255)
                                                                                                                     tttACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAGTCTGCGGCGTACAGCtt                       >  2:331793/1‑144 (MQ=255)
                                                                                                                        actacGCCAGGTCTCGTTAGCGCAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGTGGCGTACAGCTTGTc                    <  2:195750/144‑1 (MQ=255)
                                                                                                                        acgacGCCAGGTCTCGTTAGCGCAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTc                    <  2:325489/141‑1 (MQ=255)
                                                                                                                          tacGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCACTCAAACGAGAATCTGCGGCGTACAGCTTGTCgg                  >  2:308095/1‑144 (MQ=255)
                                                                                                                          aaccgcAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTCgg                  >  2:43779/6‑144 (MQ=255)
                                                                                                                                   tctcGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTCGGAGAAGGCaa         >  2:291380/1‑144 (MQ=255)
                                                                                                                                   tctcGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTCGGAGAAGGCAATCTcc    >  1:65086/1‑149 (MQ=255)
                                                                                                                                          aGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTCGGAGAAGGCAATCTCctg  <  2:264058/144‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                           
GCTTGAGGAATCCTTCGCTGGCAGCAACTTCATCTTGTAACGCAGCATCCAGACGTCC‑‑TGCAGCCAGATCGGAATAGACCAAATCCTGGTTGGCATAGGCCACCACATCCACGCCTTTACTACGCCAGGTCTCGTTAGCGTAAGCTTCCTGGGTTGATCCCTGCAGCACACCAACATGTTTACCTTTCAGTGAATCCAGCGTTGGCTGAATCGGTGAACCTTTGGCCGCAATCAAACGAGAATCTGCGGCGTACAGCTTGTCGGAGAAGGCAATCTCCTG  >  CP009273/2420691‑2420970

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑