Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,440,007 Δ1 bp 100% coding (34/201 nt) cspA_2 ← Cold shock protein CspA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,440,0070C.93.1% 170.3 / 0.8 43coding (34/201 nt)cspA_2Cold shock protein CspA
Reads supporting (aligned to +/- strand):  ref base C (0/1);  major base . (14/26);  minor base T (0/1);  total (15/28)
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  >  USA300TCH1516_ALE/1439872‑1440142
                                                                                                                                       |                                                                                                                                       
cgcgGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGtt                                                                                                                                   >  1:135366/1‑141 (MQ=255)
    gTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAAc                                                                                                                               >  2:456154/1‑141 (MQ=255)
         cTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAttt                                                                                                                          <  1:390686/141‑1 (MQ=255)
              actactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTg                                                                                                                     <  2:433824/141‑1 (MQ=255)
                  ctTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAcc                                                                                                                 >  2:74390/1‑141 (MQ=255)
                     cAAACTCATCAGCTTGATCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTg                                                                                                              <  2:138993/141‑1 (MQ=255)
                         cTCATCAGCTTGACGTTCTTCTAATGATTTGTACCCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATATAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTc                                                                                                          <  1:324671/141‑1 (MQ=255)
                               ggCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACGTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                    <  2:242138/140‑1 (MQ=255)
                               aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc                                                                                                    <  1:356697/141‑1 (MQ=255)
                                gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                   <  1:31883/141‑1 (MQ=255)
                                gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                   >  2:488923/1‑141 (MQ=255)
                                gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt                                                                                                   <  1:98540/141‑1 (MQ=255)
                                  ttGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa                                                                                                 <  1:323865/141‑1 (MQ=255)
                                  ttGACCTTCTTCTAATGATTTGTAACCAGCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa                                                                                                 <  1:389971/141‑1 (MQ=255)
                                   tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGaa                                                                                                >  1:546615/1‑141 (MQ=255)
                                     aCCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAc                                                                                              >  1:19380/1‑141 (MQ=255)
                                         tcttctAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTcc                                                                                          <  1:275172/141‑1 (MQ=255)
                                            tctAATGATTTGTAACCATCTTGGTTAATTGCTGAAACATGTACGTATACGTCATTTTCTACATAAACACTCCGAAAGCCGAATCCTCTTT‑AGCGGTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAg                                                                                       <  1:410809/141‑1 (MQ=255)
                                                 tGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTaa                                                                                  <  1:476281/141‑1 (MQ=255)
                                                       gTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcc                                                                            >  1:234086/1‑140 (MQ=255)
                                                                ttGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAACATg                                                                   <  2:234119/141‑1 (MQ=255)
                                                                 tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTGCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGc                                                                  <  1:108018/141‑1 (MQ=255)
                                                                             gAAAAATGTACGAATTCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTTTTTCATAATCTGAACCCACCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                      <  1:110697/141‑1 (MQ=255)
                                                                             gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATAC‑TTTTAAGCGTTAAACCATTTAACTGTACCTTTTTTCATAATCTGATACCTCCAAGACTAAATTTCATTGAATAGTCTAATTGGCatat                                                      >  2:544105/1‑141 (MQ=255)
                                                                                   tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAATTCATTCAATATGCTGATTCGCATATTACaaa                                                <  1:278283/141‑1 (MQ=255)
                                                                                    gTACGGATACGTCATTTTCTCCTTCAACTTCGATAAAGCCAAATCCTTTTT‑AGCGTTAAACCATTTGACTGTACCTTGTTTCATTATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaa                                               >  1:414101/1‑141 (MQ=255)
                                                                                     tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGAGTTAAACACTTTAACTGTACCTTGTTTCATAATCTAAAACCTCCAAGACTTAAATTAATTCAATATGATTATTCGCATATTACaaaaa                                              >  2:182933/1‑141 (MQ=255)
                                                                                            tcGTCATTTTCCCTGTCAACTTCGATAAAGTCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTGTCATAATCTGAAACCTCCAATACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                       <  2:378823/140‑1 (MQ=255)
                                                                                              gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTGAGACTATTTAACTGTACCGTGTTTCATAATCTGATTCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAGAAAGACATGCa                                     <  2:8102/141‑1 (MQ=255)
                                                                                                 aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCGAAt                                  >  2:375663/1‑141 (MQ=255)
                                                                                                  ttttCCCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTTAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAAtt                                 <  2:197653/141‑1 (MQ=255)
                                                                                                      ctcCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTCCAAAAACTACATGCAAATTTCAc                             >  1:531907/1‑141 (MQ=255)
                                                                                                       tacTTCAACTTCGAGAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGAATATAAAAAAAAATACATGCAAATTTCACt                            <  2:444809/139‑1 (MQ=255)
                                                                                                          ttCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaa                         >  2:52538/1‑141 (MQ=255)
                                                                                                           tCAACTTCGACAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                        <  2:180360/141‑1 (MQ=255)
                                                                                                           tCAACTTCAATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTCTTTCATAATCTGAAACCTCCAAGACTAAAATTCATCCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTGCACTCaaa                        <  2:414533/141‑1 (MQ=255)
                                                                                                                    aTAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg               >  1:62476/1‑141 (MQ=255)
                                                                                                                        aGCCGAATCCTTTTT‑AGGCTTAAACAATTTCACTGTACCTTGTTTCCTAATCTGAAACCTCCAAGACTAAAATTCATTCAACATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat           <  2:375880/141‑1 (MQ=255)
                                                                                                                           cGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATCTTACAAAAAATCCATGCACATTTTACTCAAATATTATTTGCAATATg        >  2:114405/1‑141 (MQ=255)
                                                                                                                           cGAAGCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCACACGTCACGCAAATATTCTTTGCAATATg        <  2:542571/141‑1 (MQ=255)
                                                                                                                             aaTCCTTTTT‑AGCGTTAAACCATTTAACTGCACCTTGTTTCATAATCTGAAACCACCAAGACTAAAATTCATTCAATATGCTTATTCGCAGATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGa      <  2:414101/141‑1 (MQ=255)
                                                                                                                                accgtttCTGCATTACTCCAATTAACTGTACCTTTTTTCATTATCCGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCGCATATCACAAAAAATACATGCAAACCTCACTCAAATATTCTTTGCAATATGGaat    <  2:303257/137‑1 (MQ=255)
                                                                                                                                  cttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCAAATAATAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa  <  2:45115/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                       
CGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAA  >  USA300TCH1516_ALE/1439872‑1440142

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: ‑