Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,651,744 C→T 7.8% pseudogene (194/1158 nt) intQ → pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,651,7440CT 7.8% 149.2 / 3.1 51pseudogene (194/1158 nt)intQpseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base T (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.69e-01

ACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACAACCAGGGA  >  NC_000913/1651600‑1651887
                                                                                                                                                 |                                                                                                                                               
aCTATGCAAAACAGTTTCCCTCCTCACGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCACCACATACCGTGCCGt                                                                                                                                              >  6:219351/1‑148 (MQ=255)
       aaaaCAGTTTCCCTCCTCACGCAATCTGGAAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCaa                                                                                                                                        >  6:45466/1‑148 (MQ=255)
                tCCATCGTCACGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCTCTGAAAGAATGTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTg                                                                                                                              <  2:200082/148‑1 (MQ=255)
                      ctcACGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATaa                                                                                                                       >  4:25005/1‑149 (MQ=255)
                       tcACGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAAt                                                                                                                      >  6:152390/1‑149 (MQ=255)
                         aCGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCg                                                                                                                    >  2:10702/1‑149 (MQ=255)
                                   g‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGaaaaaaa                                                                                                          >  8:19777/1‑149 (MQ=255)
                                   g‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGaaaaaaa                                                                                                          <  8:171037/149‑1 (MQ=255)
                                      aaaaTTTGGTGAGGCCCGACAAGAGTTAAACATAAAAGAACTGGCTTAAAAATTTATGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAACTc                                                                                                        <  3:127825/149‑1 (MQ=255)
                                         aTTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTg                                                                                                     <  8:55679/149‑1 (MQ=255)
                                                 aGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATc                                                                                              <  5:219351/148‑1 (MQ=255)
                                                   gCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGAt                                                                                           >  3:5851/1‑149 (MQ=255)
                                                      cGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATtaa                                                                                        >  1:155664/1‑149 (MQ=255)
                                                       gACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATtaa                                                                                        >  1:248867/1‑148 (MQ=255)
                                                          aaGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATaaa                                                                                    <  6:110212/149‑1 (MQ=255)
                                                                 aaCCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa                                                                              <  3:25005/148‑1 (MQ=255)
                                                                    cATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGTCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa                                                                              <  7:20005/145‑1 (MQ=255)
                                                                    cATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGTCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa                                                                              <  7:16301/145‑1 (MQ=255)
                                                                    cATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGTCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa                                                                              >  8:16301/1‑145 (MQ=255)
                                                                    cATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGTCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGaaaaa                                                                              >  8:20005/1‑145 (MQ=255)
                                                                    cATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTAc                                                                          >  1:247934/1‑149 (MQ=255)
                                                                             aCTGGCTGAAAAATTTCTGGCACTTAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTc                                                                 <  5:152390/149‑1 (MQ=255)
                                                                                  cTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTaaa                                                            <  1:23005/149‑1 (MQ=255)
                                                                                          tttCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTact                                                    <  8:110100/149‑1 (MQ=255)
                                                                                                gCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTactgactg                                               <  7:19777/148‑1 (MQ=255)
                                                                                                  aCTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGa                                             >  1:59932/1‑148 (MQ=255)
                                                                                                    tGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGAt                                            <  7:217244/147‑1 (MQ=255)
                                                                                                      aaagaaaCTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATAc                                          >  1:94915/1‑147 (MQ=255)
                                                                                                       aagaaaCTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATAc                                          >  8:165348/1‑146 (MQ=255)
                                                                                                        agaaaCTGAAGTCGCCAAAACATCACTCACCACATATCGTGCCGTCATCAAAAATTTCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTGCGGAAAGAGTTTCTGCCTGGCTACCa                                        >  2:243388/1‑147 (MQ=255)
                                                                                                         gaaaCTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGAt                                     <  4:39297/149‑1 (MQ=255)
                                                                                                          aaaCTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATc                                    <  2:248867/149‑1 (MQ=255)
                                                                                                                     gCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTa                          <  5:45466/148‑1 (MQ=255)
                                                                                                                      ccAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAAc                        <  2:91561/149‑1 (MQ=255)
                                                                                                                       cAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTaaa                                                            <  6:16286/112‑1 (MQ=255)
                                                                                                                       cAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTaaa                                                            >  5:16286/1‑112 (MQ=255)
                                                                                                                       cAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAAc                        >  2:202893/1‑148 (MQ=255)
                                                                                                                             aTCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTg                 >  1:223065/1‑149 (MQ=255)
                                                                                                                                aCTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTa              >  7:166577/1‑149 (MQ=255)
                                                                                                                                  tCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATACCCAAAAGTAACTATATTGTAaca            >  2:30086/1‑149 (MQ=255)
                                                                                                                                   cAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGa                                      >  4:221356/1‑122 (MQ=255)
                                                                                                                                   cAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGa                                      <  3:221356/122‑1 (MQ=255)
                                                                                                                                    aaCACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAAt                                                                             >  6:228484/1‑82 (MQ=255)
                                                                                                                                    aaCACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAAt                                                                             <  5:228484/82‑1 (MQ=255)
                                                                                                                                    aaCACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACt                       >  8:119083/1‑136 (MQ=255)
                                                                                                                                    aaCACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACt                       <  7:119083/136‑1 (MQ=255)
                                                                                                                                     acacATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACaa         <  2:94915/149‑1 (MQ=255)
                                                                                                                                      cacaTACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACAAc        <  2:223065/149‑1 (MQ=255)
                                                                                                                                       acaTACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGCCTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACAAc        >  2:171437/1‑148 (MQ=255)
                                                                                                                                       acaTACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACAAc        >  1:141584/1‑148 (MQ=255)
                                                                                                                                            ccGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACAACCAGGga  <  4:5851/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                               
ACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGG‑AAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGCACTGAAAGAAACTGAAGTCGCCAAAACATCACTCAACACATACCGTGCCGTCATCAAAAATATCCTGAGCATAATCGGTGAAAAAAATCTTGCCTCATCGATTAATAAAGAAAAATTACTGGAGGTTCGTAAAGAGTTACTGACTGGATACCAGATCCCCAAAAGTAACTATATTGTTACACAACCAGGGA  >  NC_000913/1651600‑1651887

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑