Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,371,220 C→T 22.2% G95D (GGT→GAT)  rpsJ ← 30S ribosomal protein S10

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,371,2200CT22.2% 72.1 / 16.3 36G95D (GGT→GAT) rpsJ30S ribosomal protein S10
Reads supporting (aligned to +/- strand):  ref base C (20/8);  new base T (5/3);  total (25/11)
Fisher's exact test for biased strand distribution p-value = 6.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTCTACTACTGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGATTGTGTAA  >  USA300TCH1516_ALE/2371080‑2371360
                                                                                                                                            |                                                                                                                                            
cTTCTACTACTGTTACAGGGATTAATTATCAGAGTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTacac                                                                                                                                              >  1:368767/1‑141 (MQ=255)
          tGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTaa                                                                                                                                    >  1:351308/1‑141 (MQ=255)
          tGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTaa                                                                                                                                    >  1:351377/1‑141 (MQ=255)
                  ggATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGc                                                                                                                            >  1:461585/1‑141 (MQ=255)
                     ttAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGccct                                                                                                                         >  1:653761/1‑140 (MQ=255)
                     ttAATTCACCGTTTTCTCAGCCTACTGTTGTTGGCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCa                                                                                                                         >  1:760373/1‑141 (MQ=255)
                      tAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCAt                                                                                                                        >  1:627709/1‑141 (MQ=255)
                            aCCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCAAAGATTCCTTTTTTCATCGAAAGTCCACCGCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGc                                                                                                                  <  1:144076/141‑1 (MQ=255)
                                  ttCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCTATGTCTACACCAGATGGTAAGGTTAAGCCCATTAAAACGTCAAc                                                                                                            >  1:472751/1‑141 (MQ=255)
                                            aCTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGgt                                                                                                  <  1:7699/141‑1 (MQ=255)
                                                  ttCATCCCAATTTTTCCTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTggg                                                                                            <  1:747364/140‑1 (MQ=255)
                                                  gtCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTggg                                                                                            <  1:747464/141‑1 (MQ=255)
                                                   tCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGt                                                                                           <  1:91617/141‑1 (MQ=255)
                                                      tCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTa                                                                                        >  1:668925/1‑141 (MQ=255)
                                                      tCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTa                                                                                        >  1:120430/1‑141 (MQ=255)
                                                                          aTTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTtg                                                                    <  1:7157/141‑1 (MQ=255)
                                                                               tttGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTgtgtgt                                                               >  1:579954/1‑141 (MQ=255)
                                                                                ttGGTCATCGAAAGTACACGTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTa                                                              >  1:570865/1‑141 (MQ=255)
                                                                                  ggTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACg                                                            <  1:244976/141‑1 (MQ=255)
                                                                                        cGAAAGTCCACCTCCTGAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTAGGTTGTTc                                                      >  1:453274/1‑141 (MQ=255)
                                                                                           aaGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCTACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGaa                                                   >  1:51435/1‑141 (MQ=255)
                                                                                                       tAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGCATTTTTCACGTGa                                       >  1:50988/1‑141 (MQ=255)
                                                                                                          aaTTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGGTCGAATTGTTCACGTGAATc                                    >  1:89639/1‑141 (MQ=255)
                                                                                                           aTTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAGTTGTTCACGTGAATCt                                   >  1:352083/1‑141 (MQ=255)
                                                                                                            ttGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCtt                                  >  1:208213/1‑141 (MQ=255)
                                                                                                            ttGTCTATTATAATTTGATTTCGATGTCCACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCtt                                  <  1:531504/141‑1 (MQ=255)
                                                                                                             tGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATAttt                                 >  1:251479/1‑141 (MQ=255)
                                                                                                               tCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGGCCATTAAAGCGTCAACTGTTGTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCtttct                               >  1:151323/1‑139 (MQ=255)
                                                                                                               tCTATTATAATTTGATTTCGATGTCCACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTtat                               <  1:297972/141‑1 (MQ=255)
                                                                                                                cTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTtata                              >  1:142500/1‑141 (MQ=255)
                                                                                                                cTATTATAATTTGATATCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTtata                              >  1:381673/1‑141 (MQ=255)
                                                                                                                    tataATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTa                          <  1:12461/141‑1 (MQ=255)
                                                                                                                            gATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATGAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATgcacggc                  >  1:344571/1‑141 (MQ=255)
                                                                                                                               ttCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATgcacggcacg               <  1:618643/141‑1 (MQ=255)
                                                                                                                                  gATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGgat            >  1:534314/1‑141 (MQ=255)
                                                                                                                                       cTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGATtg       >  1:698954/1‑141 (MQ=255)
                                                                                                                                        tACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGATtgt      >  1:428423/1‑141 (MQ=255)
                                                                                                                                            ccAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTGCGTTGTGGGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGATTGTGTaa  >  1:62036/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
CTTCTACTACTGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGATTGTGTAA  >  USA300TCH1516_ALE/2371080‑2371360

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: ‑