Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,777,419:1 +A 100% coding (3964/4581 nt) ypjA ← adhesin‑like autotransporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,777,4191.A86.7% 115.1 / 15.9 45coding (3964/4581 nt)ypjAadhesin‑like autotransporter
Reads supporting (aligned to +/- strand):  ref base . (2/4);  new base A (10/29);  total (12/33)
Fisher's exact test for biased strand distribution p-value = 6.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

TTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATATC  >  W3110S.gb/2777354‑2777485
                                                                  |                                                                  
ttCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaa                                                                 >  1:2811165/1‑69 (MQ=255)
 tCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaa                                                                 >  1:2142565/1‑68 (MQ=255)
  cATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaaa                                                                >  1:2800152/1‑68 (MQ=255)
   aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaaaa                                                               >  1:3284173/1‑67 (MQ=255)
   aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaaaa                                                               >  1:2067013/1‑67 (MQ=255)
   aTGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaaa                                                                <  1:1563876/67‑1 (MQ=255)
    tGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaaaac                                                              <  1:1852333/68‑3 (MQ=255)
    tGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCaaaaac                                                              <  1:1930606/68‑3 (MQ=255)
     gTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAACCGa                                                            <  1:1424397/69‑1 (MQ=255)
      ttCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCa                                                                   >  1:2934341/1‑61 (MQ=255)
           aaCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAACCGATAtgtg                                                      <  1:173066/69‑1 (MQ=255)
            aCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:465049/69‑1 (MQ=255)
            aCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:1494336/69‑1 (MQ=255)
            aCTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:1762877/69‑1 (MQ=255)
                  aTAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg                                                  <  1:2230108/67‑1 (MQ=255)
                  aTAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg                                                  <  1:1713309/67‑1 (MQ=255)
                  aTAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg                                                  <  1:118983/67‑1 (MQ=255)
                   tAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATg                                                  <  1:3653466/66‑1 (MQ=255)
                   tAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGa                                               <  1:3174470/69‑1 (MQ=255)
                   tAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGa                                               <  1:2614926/69‑1 (MQ=255)
                     gccgccCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:3542582/60‑1 (MQ=255)
                           cAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                >  1:3238376/1‑60 (MQ=255)
                           cAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                >  1:202616/1‑60 (MQ=255)
                               gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:2455141/50‑1 (MQ=255)
                               gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:3659112/50‑1 (MQ=255)
                               gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:2708942/50‑1 (MQ=255)
                               gaATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATaaa                                   >  1:2451976/1‑69 (MQ=255)
                                aaTAACTGCCCACACTGCCATGTCCTCCGCGATCAAAACCGATATGTGAATGGGAATAGCCCATAAAAg                                 >  1:15855/1‑69 (MQ=255)
                                    aCTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                <  1:2162677/51‑1 (MQ=255)
                                    aCTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                <  1:269259/51‑1 (MQ=255)
                                    aCTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                <  1:1207182/51‑1 (MQ=255)
                                     cTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATaaa                                   >  1:3172732/1‑63 (MQ=255)
                                     cTGCCCACACTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATaaa                                   >  1:701123/1‑63 (MQ=255)
                                              cTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:1073237/35‑1 (MQ=37)
                                              cTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      <  1:3405133/35‑1 (MQ=37)
                                              cTGCCATGTCCTCCGCGATCAAAAACCGATAtgtg                                                      >  1:3195683/1‑35 (MQ=37)
                                              cTGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt                    <  1:3678702/69‑1 (MQ=255)
                                               tGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt                    <  1:663140/68‑1 (MQ=255)
                                               tGCCATGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGt                    >  1:898781/1‑68 (MQ=255)
                                                 ccATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                <  1:3128908/38‑1 (MQ=38)
                                                 ccATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                <  1:2686176/38‑1 (MQ=38)
                                                 ccATGTCCTCCGCGATCAAAAACCGATATGTGAATggg                                                <  1:732309/38‑1 (MQ=38)
                                                   ctGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt                 <  1:1964948/66‑1 (MQ=255)
                                                   aTGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt                 <  1:1470763/67‑1 (MQ=255)
                                                   aTGTCCTCCGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAAt                 <  1:2145982/67‑1 (MQ=255)
                                                      tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATa                                     >  1:3188072/1‑44 (MQ=38)
                                                      tcctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATa                                     >  1:494145/1‑44 (MQ=38)
                                                        ctccGCGATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTc           <  1:684843/68‑1 (MQ=255)
                                                           cgcgATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAgg        >  1:1400860/1‑68 (MQ=255)
                                                             cgATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAgg        <  1:2452238/66‑1 (MQ=255)
                                                             cgATCAAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAgg        <  1:2334426/66‑1 (MQ=255)
                                                              gATCAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAatat   <  1:437714/69‑1 (MQ=255)
                                                              gATCAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAatat   <  1:2381317/69‑1 (MQ=255)
                                                                tCAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATATc  >  1:2211752/1‑68 (MQ=255)
                                                                  |                                                                  
TTCATGTTCCCAACTGGCATAGCCGCCCAGAGAATAACTGCCCACACTGCCATGTCCTCCGCGATCAAAACCGATATGTGAATGGGAATAGCCCATAAAAGCGCCTAGCGTGGTAATTCCTTCAGGAATATC  >  W3110S.gb/2777354‑2777485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: