Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,981,418 C→A intergenic (‑17/+339) USA300HOU_RS09870 ← / ← liaR hypothetical protein/Transcriptional regulatory protein LiaR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,981,4180CA94.9% 120.4 / 1.7 39intergenic (‑17/+339)USA300HOU_RS09870/liaRhypothetical protein/Transcriptional regulatory protein LiaR
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base A (12/25);  total (14/25)
Fisher's exact test for biased strand distribution p-value = 1.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.58e-01

GATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTCAACAAGAGT  >  USA300TCH1516_ALE/1981276‑1981560
                                                                                                                                              |                                                                                                                                              
gATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGttt                                                                                                                                           <  2:221578/148‑1 (MQ=255)
gATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGttt                                                                                                                                           <  1:165086/148‑1 (MQ=255)
gATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGttt                                                                                                                                           <  1:352837/148‑1 (MQ=255)
    tGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTgggg                                                                                                                                       <  1:140723/148‑1 (MQ=255)
    tGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTgggg                                                                                                                                       <  2:272247/148‑1 (MQ=255)
    tGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTgggg                                                                                                                                       <  1:345285/148‑1 (MQ=255)
        cTAAAGTNTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAAtt                                                                                                                                   <  2:289506/148‑1 (MQ=255)
           aaGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTa                                                                                                                                <  1:125294/148‑1 (MQ=255)
           aaGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTa                                                                                                                                >  1:55469/1‑148 (MQ=255)
           aaGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTa                                                                                                                                <  1:54535/148‑1 (MQ=255)
           aaGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTa                                                                                                                                <  1:27116/148‑1 (MQ=255)
             gTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATc                                                                                                                              <  2:62581/148‑1 (MQ=255)
                     aGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAGACTCTGTCTATCCATTCTGTTATCTGCCTTTATGTTTGGGGAATTTTATCCGGAcaca                                                                                                                      <  2:48053/148‑1 (MQ=255)
                                        gcCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATacac                                                                                                   >  2:287543/1‑148 (MQ=255)
                                        gcCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATacac                                                                                                   >  2:229388/1‑148 (MQ=255)
                                                     gCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAaca                                                                                      <  1:158003/148‑1 (MQ=255)
                                                           aaCCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGAtt                                                                                >  2:380461/1‑148 (MQ=255)
                                                             ccAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTAc                                                                              >  2:7476/1‑148 (MQ=255)
                                                             ccAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTAc                                                                              >  2:211318/1‑148 (MQ=255)
                                                             ccAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTAc                                                                              <  1:9847/148‑1 (MQ=255)
                                                             ccAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTAc                                                                              >  1:44102/1‑148 (MQ=255)
                                                                gCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATc                                                                           <  1:37403/148‑1 (MQ=255)
                                                                gCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTAATCTTACGGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATc                                                                           <  1:298245/148‑1 (MQ=255)
                                                                       taCGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAatat                                                                    <  1:64045/148‑1 (MQ=255)
                                                                                ttttAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTtaat                                                           >  2:274778/1‑148 (MQ=255)
                                                                                             ttgAATTAAATCTGTAACACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTGGGGGAATGATATCCGGACACAAGAAATTGCAAAAATACACATTTCTAGAAATACAAATAACATATTAAAATAATTTTAATAAAATGAAAagag                                              <  2:294742/148‑1 (MQ=255)
                                                                                             ttgAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAagag                                              >  2:189114/1‑148 (MQ=255)
                                                                                                              aaCTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCCTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTa                             <  1:204495/148‑1 (MQ=255)
                                                                                                                         tCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGa                  <  1:103973/148‑1 (MQ=255)
                                                                                                                           cATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGCCACAAGAAATTGCAATAAAACACAACTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATc                <  1:174303/148‑1 (MQ=255)
                                                                                                                           cATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATc                <  2:184431/148‑1 (MQ=255)
                                                                                                                               cTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTTTTTTTTTTTTAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGt            >  2:268133/1‑148 (MQ=255)
                                                                                                                               cTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGt            <  1:39169/148‑1 (MQ=255)
                                                                                                                               cTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGt            >  2:341300/1‑148 (MQ=255)
                                                                                                                                    aTCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTcaaca       <  1:326546/148‑1 (MQ=255)
                                                                                                                                        aCCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGGCAACAagag   <  2:55469/148‑1 (MQ=255)
                                                                                                                                         ccTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTCAACAAGAGt  >  2:28254/1‑148 (MQ=255)
                                                                                                                                         ccTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTCAACAAGAGt  >  2:28490/1‑148 (MQ=255)
                                                                                                                                         ccTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTCAACAAGAGt  >  2:33211/1‑148 (MQ=255)
                                                                                                                                              |                                                                                                                                              
GATTTGTACTAAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTCAACAAGAGT  >  USA300TCH1516_ALE/1981276‑1981560

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑