Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,638,557 A→T 9.5% I37I (ATT→ATA)  cspI ← Qin prophage; cold shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,638,5570AT 9.5% 120.5 / 2.8 42I37I (ATT→ATA) cspIQin prophage; cold shock protein
Reads supporting (aligned to +/- strand):  ref base A (25/13);  new base T (2/2);  total (27/15)
Fisher's exact test for biased strand distribution p-value = 6.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

GGCATCTAAAGTGAATATGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGG  >  NC_000913/1638417‑1638699
                                                                                                                                            |                                                                                                                                              
ggCATCTAAAGTGAATATGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTga                                                                                                                                        <  2:195719/149‑1 (MQ=255)
 gCATCTAAAGTGAATATGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTgag                                                                                                                                       >  1:301849/1‑149 (MQ=255)
       aaaGTGAATATGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATgg                                                                                                                                 >  2:68089/1‑149 (MQ=255)
       aaaGTGAATATGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTACTGAGAAATgg                                                                                                                                 >  1:314635/1‑149 (MQ=255)
                 tGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTGCCGGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACAt                                                                                                                       <  1:691788/149‑1 (MQ=255)
                           tatTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGcc                                                                                                             <  2:237691/149‑1 (MQ=255)
                                  tACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTc                                                                                                      >  1:12727/1‑149 (MQ=255)
                                     cTCAAAGCGCCACTACATGAACCGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTCATGTTTTGAAATCGCTGCCCTCAACTGCCCAGAAATGGACAAACACAACTTTGCTGCCATCtcccgcc                                                                                                   >  2:417858/1‑143 (MQ=255)
                                        aaaGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGtg                                                                                                >  2:317391/1‑149 (MQ=255)
                                             gcCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGCGATGaa                                                                                           >  1:569956/1‑149 (MQ=255)
                                             gcCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCATGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGGGAGGaa                                                                                           >  1:569947/1‑149 (MQ=255)
                                              tcACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGaaa                                                                                          <  2:231725/148‑1 (MQ=255)
                                              ccACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGaaa                                                                                          <  1:366331/149‑1 (MQ=255)
                                              ccAATACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGaaa                                                                                          <  1:562546/149‑1 (MQ=255)
                                                    cATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGTATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCaaaa                                                                                    >  2:284628/1‑149 (MQ=255)
                                                    cATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCAGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGTATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCaaaa                                                                                    >  2:401872/1‑149 (MQ=255)
                                                      tGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTAGGCGTGATGAAACCAAAAcc                                                                                  >  1:14991/1‑149 (MQ=255)
                                                          cAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCtttt                                                                              >  2:387721/1‑149 (MQ=255)
                                                           aGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGGGATGAAACCAAAACCttttt                                                                             >  1:695238/1‑149 (MQ=255)
                                                                    aCCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTaa                                                                    <  1:702474/149‑1 (MQ=255)
                                                                        ttAGGTCCGTTCTCAATACCAAATGCAACTTCCGGATTCTCAGTTAATGTTTGGAAATCGGTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCa                                                                <  2:37892/149‑1 (MQ=255)
                                                                             tCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa                                                           >  1:661320/1‑149 (MQ=255)
                                                                              ccGTTCTCAATACCAAATTCAACGTCCTAATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc                                                          >  1:404837/1‑149 (MQ=255)
                                                                                 ttCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa                                                       >  1:89921/1‑149 (MQ=255)
                                                                                    tcAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAACCACATCTTTGCTGCCGTCTTTCGGCGTGATGAAACCAAAACCTTTTCCAGGGTTACACCATCTGACTAAAcc                                                    >  1:81571/1‑149 (MQ=255)
                                                                                      aaTACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAg                                                  >  1:504994/1‑149 (MQ=255)
                                                                                          ccAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAt                                              >  2:172805/1‑149 (MQ=255)
                                                                                          ccAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAt                                              >  2:172842/1‑149 (MQ=255)
                                                                                           cAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCagt                                             >  1:68619/1‑147 (MQ=255)
                                                                                           cAAATTCAACTTCCGTATTCTTAGTTAATGTTTTAAAATCGTTGCTCTAAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt                                             <  2:583949/149‑1 (MQ=255)
                                                                                               ttCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                         <  2:449124/149‑1 (MQ=255)
                                                                                                  aaCTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAg                                      >  1:342400/1‑149 (MQ=255)
                                                                                                  aaCTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACGAAACCAGTCATTTTGTTAg                                      <  2:497492/149‑1 (MQ=255)
                                                                                                         tGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                               >  2:717373/1‑149 (MQ=255)
                                                                                                                  gTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt                      >  1:337903/1‑149 (MQ=255)
                                                                                                                   ttAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAAACTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCttt                     >  1:495346/1‑149 (MQ=255)
                                                                                                                          tttGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa              >  1:606867/1‑149 (MQ=255)
                                                                                                                           ttGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGaaa             >  1:703796/1‑149 (MQ=255)
                                                                                                                            tGAAATTGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCGTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt            <  1:323552/149‑1 (MQ=255)
                                                                                                                                     tGCTCTGTATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTg   <  1:401872/149‑1 (MQ=255)
                                                                                                                                     tGCTCTGTATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTg   <  1:284628/149‑1 (MQ=255)
                                                                                                                                      gCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTgg  <  1:563525/149‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                              
GGCATCTAAAGTGAATATGGTTTGTAATATTGTCTACCTCAAAGCGCCACTACATGAACAGCGGCAGGACCTTTAGGTCCGTTCTCAATACCAAATTCAACTTCCTGATTCTCAGTTAATGTTTTGAAATCGTTGCTCTGAATTGCTGAGAAATGGACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGG  >  NC_000913/1638417‑1638699

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑