Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,094,261 A→G 14.3% T553T (ACT→ACC USA300HOU_RS10605 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,094,2610AG14.3% 105.2 / 11.5 42T553T (ACT→ACCUSA300HOU_RS10605hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (17/19);  new base G (3/3);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.81e-01

GTGGATTCTCTAGCTGCTTCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTACCAACCGACCAATCGTTGC  >  USA300TCH1516_ALE/2094133‑2094398
                                                                                                                                |                                                                                                                                         
gtgGATTCTCTAGCTGCTTCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGAc                                                                                                                               <  1:391525/141‑1 (MQ=255)
 tgGATTCTCTAGCTGCTTCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACt                                                                                                                              >  1:378001/1‑141 (MQ=255)
     ttCTCTAGCTGCTTCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGtaa                                                                                                                          <  2:221179/141‑1 (MQ=255)
        tctAGCTGCTTCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGtaataa                                                                                                                       <  1:139490/141‑1 (MQ=255)
                  tCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAatcta                                                                                                             <  1:207441/141‑1 (MQ=255)
                  tCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAatcta                                                                                                             <  2:395238/141‑1 (MQ=255)
                    aaTAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAatctatc                                                                                                           >  1:7504/1‑141 (MQ=255)
                    aaTAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAatctatc                                                                                                           >  1:242088/1‑141 (MQ=255)
                       aGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGa                                                                                                        >  1:262111/1‑141 (MQ=255)
                          tGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAAt                                                                                                     <  1:456255/141‑1 (MQ=255)
                             tttAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCGGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGc                                                                                                  >  1:201071/1‑141 (MQ=255)
                             tttAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCGGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGc                                                                                                  >  1:420446/1‑141 (MQ=255)
                             tttAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCGGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGc                                                                                                  >  1:167789/1‑141 (MQ=255)
                             tttAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGc                                                                                                  >  1:172332/1‑141 (MQ=255)
                                     caTTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGa                                                                                          <  2:265925/141‑1 (MQ=255)
                                     caTTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGa                                                                                          >  2:282331/1‑141 (MQ=255)
                                                ccGACTAACTGCAAATCTTCATTCACCGTTAATCCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTTTAATAATTTAAATCTAGCTGAAATGGCGATTTTGACATCTTCTACa                                                                               <  2:370718/141‑1 (MQ=255)
                                                          gCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATaaa                                                                     >  2:137044/1‑141 (MQ=255)
                                                                   cattcaCCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTa                                                            <  2:262111/141‑1 (MQ=255)
                                                                    tttcaCCGTTTAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGTCTGTAATAATTTTAATCTATCTGAAATGGCGATTTTGACTTCTTCTACATCTGTATAAACATCgtgtgt                                                           <  2:137042/140‑3 (MQ=255)
                                                                    attcaCCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTaa                                                           <  2:115360/141‑1 (MQ=255)
                                                                             tAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATttctttct                                                  >  1:230795/1‑141 (MQ=255)
                                                                               aaCCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCtat                                                >  2:261277/1‑141 (MQ=255)
                                                                               aaCCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCtat                                                >  2:257313/1‑141 (MQ=255)
                                                                                     aTTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCaa                                          <  1:305734/141‑1 (MQ=255)
                                                                                       tttGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATTATTTAAATCTGTCTGAAATGGGGATTTTGACATCTTTTACATCTGTATAAACATCTTTTAATTTCTTTCTATACTCAAGa                                        >  1:72258/1‑141 (MQ=255)
                                                                                       tttGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGa                                        >  1:354069/1‑141 (MQ=255)
                                                                                       tttGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGa                                        >  1:16850/1‑141 (MQ=255)
                                                                                        ttgttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGaa                                       >  1:203386/1‑141 (MQ=255)
                                                                                          gttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAAt                                     <  2:395297/141‑1 (MQ=255)
                                                                                          gttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAAt                                     <  1:152851/141‑1 (MQ=255)
                                                                                          gttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAAt                                     <  1:96561/141‑1 (MQ=255)
                                                                                          gttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAAt                                     <  1:300436/141‑1 (MQ=255)
                                                                                          gttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAAt                                     <  1:253703/141‑1 (MQ=255)
                                                                                          gttgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAAt                                     <  1:252192/141‑1 (MQ=255)
                                                                                            tgCTATTATTTCCAACGCTTCTTTATATTTTTCATCGGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATaa                                   <  2:201071/141‑1 (MQ=255)
                                                                                            tgCTATTATTTCCAACGCTTCTTTATATTTTTCATCGGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATaa                                   <  2:167789/141‑1 (MQ=255)
                                                                                            tgCTATTATTTCCAACGCTTCTTTATATTTTTCATCGGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATaa                                   <  2:420446/141‑1 (MQ=255)
                                                                                            tgCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATaa                                   >  2:387941/1‑141 (MQ=255)
                                                                                                          aCGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTa                     >  1:300782/1‑141 (MQ=255)
                                                                                                           cGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTAc                    <  2:288961/141‑1 (MQ=255)
                                                                                                             cttcttTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTACCa                  >  2:362717/1‑141 (MQ=255)
                                                                                                                            catcaGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTACCAACCGACCAATCGTTg   <  2:23398/141‑1 (MQ=255)
                                                                                                                            catcaGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTACCAACCGACCAATCGTTg   <  2:442045/141‑1 (MQ=255)
                                                                                                                             atcaGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTACCAACCGACCAATCGTTGc  >  1:81853/1‑141 (MQ=255)
                                                                                                                             atcaGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACACAAGAAATAAAGTTTTTGTATCTACCAACCGACCAATCGTTGc  >  1:361369/1‑141 (MQ=255)
                                                                                                                                |                                                                                                                                         
GTGGATTCTCTAGCTGCTTCAATAGCTGATTTAACAACATTAGGTTCTCCGACTAACTGCAAATCTTCATTCACCGTTAAACCAAATTTTGTTGCTATTATTTCCAACGCTTCTTTATATTTTTCATCAGTGTATTGTGACTGTAATAATTTAAATCTATCTGAAATGGCGATTTTGACATCTTCTACATCTGTATAAACATCTTGTAATTTCTTTCTATACTCAAGAAATAAAGTTTTTGTATCTACCAACCGACCAATCGTTGC  >  USA300TCH1516_ALE/2094133‑2094398

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