Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,440,007 Δ1 bp 100% coding (34/201 nt) cspA ← cold shock protein CspA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0070C.93.4% 180.3 / 0.7 45coding (34/201 nt)cspAcold shock protein CspA
Reads supporting (aligned to +/- strand):  ref base C (0/1);  major base . (14/28);  minor base T (0/1);  total (15/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

CGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAA  >  CP000730/1439872‑1440142
                                                                                                                                       |                                                                                                                                       
cgcgGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGtt                                                                                                                                   >  1:135366/1‑141 (MQ=255)
    gTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAAc                                                                                                                               >  2:456154/1‑141 (MQ=255)
         cTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCAttt                                                                                                                          <  1:390686/141‑1 (MQ=255)
              actactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTg                                                                                                                     <  2:433824/141‑1 (MQ=255)
                  ctTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTAcc                                                                                                                 >  2:74390/1‑141 (MQ=255)
                     cAAACTCATCAGCTTGATCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTg                                                                                                              <  2:138993/141‑1 (MQ=255)
                         cTCATCAGCTTGACGTTCTTCTAATGATTTGTACCCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATATAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTc                                                                                                          <  1:324671/141‑1 (MQ=255)
                               ggCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACGTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                    <  2:242138/140‑1 (MQ=255)
                               aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                    <  1:356697/141‑1 (MQ=255)
                                gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                   <  1:31883/141‑1 (MQ=255)
                                gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                   >  2:488923/1‑141 (MQ=255)
                                gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                   <  1:98540/141‑1 (MQ=255)
                                  ttGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa                                                                                                 <  1:323865/141‑1 (MQ=255)
                                  ttGACCTTCTTCTAATGATTTGTAACCAGCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa                                                                                                 <  1:389971/141‑1 (MQ=255)
                                   tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGaa                                                                                                >  1:546615/1‑141 (MQ=255)
                                     aCCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAc                                                                                              >  1:19380/1‑141 (MQ=255)
                                         tcttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTcc                                                                                          <  1:275172/141‑1 (MQ=255)
                                            tctAATGATTTGTAACCATCTTGGTTAATTGCTGAAACATGTACGTATACGTCATTTTCTACATAAACACTCCGAAAGCCGAATCCTCTTTAGCGGTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAg                                                                                       <  1:410809/141‑1 (MQ=255)
                                                 tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                  <  1:476281/141‑1 (MQ=255)
                                                       gtaacctgctgtgTTCATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTGCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattca                                                                            <  1:145020/129‑1 (MQ=255)
                                                       gTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcc                                                                            >  1:234086/1‑140 (MQ=255)
                                                                ttGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAACATg                                                                   <  2:234119/141‑1 (MQ=255)
                                                                 tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTGCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGc                                                                  <  1:108018/141‑1 (MQ=255)
                                                                             gAAAAATGTACGAATTCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTTTTTCATAATCTGAACCCACCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                      <  1:110697/141‑1 (MQ=255)
                                                                             gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATACTTTTAAGCGTTAAACCATTTAACTGTACCTTTTTTCATAATCTGATACCTCCAAGACTAAATTTCATTGAATAGTCTAATTGGCatat                                                      >  2:544105/1‑141 (MQ=255)
                                                                                   tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAATTCATTCAATATGCTGATTCGCATATTACaaa                                                <  1:278283/141‑1 (MQ=255)
                                                                                    gTACGGATACGTCATTTTCTCCTTCAACTTCGATAAAGCCAAATCCTTTTTAGCGTTAAACCATTTGACTGTACCTTGTTTCATTATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaa                                               >  1:414101/1‑141 (MQ=255)
                                                                                     tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGAGTTAAACACTTTAACTGTACCTTGTTTCATAATCTAAAACCTCCAAGACTTAAATTAATTCAATATGATTATTCGCATATTACaaaaa                                              >  2:182933/1‑141 (MQ=255)
                                                                                            tcGTCATTTTCCCTGTCAACTTCGATAAAGTCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTGTCATAATCTGAAACCTCCAATACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                       <  2:378823/140‑1 (MQ=255)
                                                                                              gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTGAGACTATTTAACTGTACCGTGTTTCATAATCTGATTCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAGAAAGACATGCa                                     <  2:8102/141‑1 (MQ=255)
                                                                                                 aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCGAAt                                  >  2:375663/1‑141 (MQ=255)
                                                                                                  ttttCCCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTTAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAAtt                                 <  2:197653/141‑1 (MQ=255)
                                                                                                      ctcCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTCCAAAAACTACATGCAAATTTCAc                             >  1:531907/1‑141 (MQ=255)
                                                                                                       tacTTCAACTTCGAGAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGAATATAAAAAAAAATACATGCAAATTTCACt                            <  2:444809/139‑1 (MQ=255)
                                                                                                         cttccactcgcaTAAAGCCCAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCa                          <  1:25060/130‑1 (MQ=255)
                                                                                                          ttCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaa                         >  2:52538/1‑141 (MQ=255)
                                                                                                           tCAACTTCGACAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                        <  2:180360/141‑1 (MQ=255)
                                                                                                           tCAACTTCAATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTCTTTCATAATCTGAAACCTCCAAGACTAAAATTCATCCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTGCACTCaaa                        <  2:414533/141‑1 (MQ=255)
                                                                                                                    aTAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg               >  1:62476/1‑141 (MQ=255)
                                                                                                                        aGCCGAATCCTTTTTAGGCTTAAACAATTTCACTGTACCTTGTTTCCTAATCTGAAACCTCCAAGACTAAAATTCATTCAACATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat           <  2:375880/141‑1 (MQ=255)
                                                                                                                           cGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATCTTACAAAAAATCCATGCACATTTTACTCAAATATTATTTGCAATATg        >  2:114405/1‑141 (MQ=255)
                                                                                                                           cGAAGCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCACACGTCACGCAAATATTCTTTGCAATATg        <  2:542571/141‑1 (MQ=255)
                                                                                                                             aaTCCTTTTTAGCGTTAAACCATTTAACTGCACCTTGTTTCATAATCTGAAACCACCAAGACTAAAATTCATTCAATATGCTTATTCGCAGATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGa      <  2:414101/141‑1 (MQ=255)
                                                                                                                                accgtttCTGCATTACTCCAATTAACTGTACCTTTTTTCATTATCCGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCGCATATCACAAAAAATACATGCAAACCTCACTCAAATATTCTTTGCAATATGGaat    <  2:303257/137‑1 (MQ=255)
                                                                                                                                  cttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCAAATAATAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa  <  2:45115/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAA  >  CP000730/1439872‑1440142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: