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.95.5% 90.9 / ‑1.5 22coding (34/201 nt)cspAcold shock protein CspA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base . (12/9);  minor base T (1/0);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-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.

CGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT  >  CP000730/1439872‑1440140
                                                                                                                                       |                                                                                                                                     
cgcgGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGt                                                                                                                                  >  1:61654/1‑140 (MQ=255)
                tactTCAAACTCAACAGCTTTACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCGTTTTAGCGTTAAACCATTTAACTga                                                                                                                  >  1:215706/1‑139 (MQ=255)
                 actTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTa                                                                                                                 <  1:71080/140‑1 (MQ=255)
                         cTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTGGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGttt                                                                                                         >  2:178019/1‑140 (MQ=255)
                           cAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCa                                                                                                       <  1:192195/140‑1 (MQ=255)
                                                aTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACt                                                                                  <  1:8868/140‑1 (MQ=255)
                                                            cATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTCACTGTACCTTTTTTCATAATCTGAAACCTACAATACTAAAAttcattca                                                                      >  2:313774/1‑140 (MQ=255)
                                                                 tgtttAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATg                                                                 <  2:100563/137‑1 (MQ=255)
                                                                 tGGTTAATTGCTGAAAAATGTACGAATACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATg                                                                 >  2:59144/1‑140 (MQ=255)
                                                                 tGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATg                                                                 <  2:14892/140‑1 (MQ=255)
                                                                      aaTTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAGAGCCGAATCCTCTTTAGCGTTAAACCATTTAGCTGTACCTTTTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAt                                                            <  2:2470/140‑1 (MQ=255)
                                                                             gAAAAATGTACGAATACGTCTTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAGTTCATTCAATATGCTTATTCGCata                                                     >  1:215364/1‑140 (MQ=255)
                                                                             gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCata                                                     >  1:341/1‑140 (MQ=255)
                                                                                  aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCACTCAATATGCCTATTCGCATATTACa                                                <  1:178019/140‑1 (MQ=255)
                                                                                   tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaa                                               >  1:280825/1‑140 (MQ=255)
                                                                                   tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCAAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGGCTAAAATTCATTCAATATGCTTATTGGCATATTACaa                                               >  1:143341/1‑140 (MQ=255)
                                                                                     tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaa                                             >  2:181169/1‑140 (MQ=255)
                                                                                            aCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACAt                                      >  2:207367/1‑140 (MQ=255)
                                                                                                           tCAACTTCGATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAGAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaa                       >  2:176857/1‑140 (MQ=255)
                                                                                                                   gATAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt               <  2:306401/140‑1 (MQ=255)
                                                                                                                     tAAAGCCGAATCCTTTTTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAATCCTCCAAGACTAAAATTCATTTAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg             <  1:203642/140‑1 (MQ=255)
                                                                                                                                 ccttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat  >  2:354772/3‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                     
CGCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT  >  CP000730/1439872‑1440140

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: