Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,514,843 G→A 13.8% Y319Y (TAC→TAT)  rlmL ← Ribosomal RNA large subunit methyltransferase L

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,514,8430GA13.8% 69.8 / 3.9 29Y319Y (TAC→TAT) rlmLRibosomal RNA large subunit methyltransferase L
Reads supporting (aligned to +/- strand):  ref base G (16/9);  new base A (2/2);  total (18/11)
Fisher's exact test for biased strand distribution p-value = 6.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.30e-01

ATATATCCATTAAATAACTTACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATCAGACAATCCAA  >  USA300TCH1516_ALE/1514715‑1514982
                                                                                                                                |                                                                                                                                           
atatatCCATTAAATAACTTACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCa                                                                                                                                 <  1:66678/141‑1 (MQ=255)
atatatCCATTAAATAACTTAAGTTTCGTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCa                                                                                                                                 >  2:182254/1‑141 (MQ=255)
                  ttACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTGCTTGTTGAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGATACATTTCTTCAACTTCTTCACGATCACCa                                                                                                               >  1:372704/1‑141 (MQ=255)
                  ttACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCa                                                                                                               >  1:254627/1‑141 (MQ=255)
                  ttACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGATACATTTCTTCAACTTCTTCACGATCACCa                                                                                                               >  1:45332/1‑141 (MQ=255)
                    aCGTCGCTTTGTCGCTTTACTCGCTACTAAATATTCAAATTCTTTATTACTTGTTTAAATGTTTTTAGATTTAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAAt                                                                                                             <  2:352349/141‑1 (MQ=255)
                     cGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCATGATCACCAAtt                                                                                                            >  2:214861/1‑140 (MQ=255)
                           tttGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTTTTCACGATCACCAATACGTTCa                                                                                                      >  2:113816/1‑141 (MQ=255)
                                tgCTTTACGATCTACAAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTCCCGATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCatc                                                                                                 >  1:292026/1‑140 (MQ=255)
                                             actaAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCa                                                                                    <  1:182254/141‑1 (MQ=255)
                                                     ttCAAATTCTTTATTTCTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATTCGTTCACCATATGGAGGATTTCCAATTAACGc                                                                            <  2:233592/141‑1 (MQ=255)
                                                     ttCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGATACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGc                                                                            <  2:45332/141‑1 (MQ=255)
                                                     taacaaTTCATTAATACTGGCTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGATACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGc                                                                            <  2:372704/137‑1 (MQ=255)
                                                               ttattaCTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGttct                                                                  >  1:231594/1‑141 (MQ=255)
                                                               ttattaCTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGttct                                                                  >  1:394749/1‑141 (MQ=255)
                                                                    aCTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGt                                                             >  2:115712/1‑141 (MQ=255)
                                                                      ttgttgAAATTTATGTAGATAAAAATGGATGTCGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTAt                                                           <  2:71800/141‑1 (MQ=255)
                                                                                       gATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCACCTTCTTCACGATCACCAATACGTTCACCATATGGAGGTTTTCCAATTAACGCCACCGGTTCTTCTGTCTCAATTGTTAATGTATTg                                          >  1:15518/1‑141 (MQ=255)
                                                                                            aaaTGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATc                                     >  2:286187/1‑141 (MQ=255)
                                                                                              aTGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTACCGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGCCATCtt                                   >  2:106505/1‑141 (MQ=255)
                                                                                               tGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCttt                                  <  2:140065/141‑1 (MQ=255)
                                                                                               tGGATGTTGTTTCATTAGTTTACCAATACAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCttt                                  <  1:275080/141‑1 (MQ=255)
                                                                                                ggATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCtttt                                 >  1:309232/1‑141 (MQ=255)
                                                                                                ggATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCtttt                                 >  1:281129/1‑141 (MQ=255)
                                                                                                     ttgttTCATGAGTTTACCAATAGAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACt                            <  1:104131/141‑1 (MQ=255)
                                                                                                      tgttTCATTATTTGACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCTCCCTAGGGTGGTTTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTa                           <  1:390185/141‑1 (MQ=255)
                                                                                                                         tataACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATCAGACa        >  2:238010/1‑141 (MQ=255)
                                                                                                                         tataACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATCAGACa        >  2:360633/1‑141 (MQ=255)
                                                                                                                             aCGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATAAGACaaaca    >  2:236224/1‑138 (MQ=255)
                                                                                                                               ggTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATCAGACAATCCaa  >  2:126104/1‑141 (MQ=255)
                                                                                                                               ggTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATCAGACAATCCaa  >  1:330915/1‑141 (MQ=255)
                                                                                                                                |                                                                                                                                           
ATATATCCATTAAATAACTTACGTCGCTTTGTTGCTTTACGATCTACTAAATATTCAAATTCTTTATTACTTGTTAAAATGTATGTAGATAAAAATGGATGTTGTTTCATTAGTTTACCAATATAACGGTACATTTCTTCAACTTCTTCACGATCACCAATACGTTCACCATATGGAGGATTTCCAATTAACGCCACCGGTTCTTCTGTATCAATTGTTAATGTATTGACATCTTTTACACTAAATTTAATAATATCAGACAATCCAA  >  USA300TCH1516_ALE/1514715‑1514982

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑