Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F169 I1 R1 62 44.4 970160 98.1% 951726 147.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,086,905 (A)8→7 intergenic (‑56/‑629) scn_3 ← / → chp Staphylococcal complement inhibitor/Chemotaxis inhibitory protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,086,8980A.97.2% 155.2 / ‑1.6 36intergenic (‑49/‑636)scn_3/chpStaphylococcal complement inhibitor/Chemotaxis inhibitory protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (21/14);  total (21/15)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

CTAGCTTGTGCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAA  >  USA300TCH1516_ALE/2086755‑2087041
                                                                                                                                               |                                                                                                                                               
cTAGCTTGTGCATCATGTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTaaaaa                                                                                                                                             <  4:47894/148‑1 (MQ=255)
    cTTGTGCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTaa                                                                                                                                                <  1:64904/141‑1 (MQ=255)
       gtgCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACa                                                                                                                                     >  4:1579/1‑148 (MQ=255)
                  ttATATAGATTAGTTAATAGAGGAGATGCTAAAATGATTGTTAAAGTTCCCGAAAGTATAGATTTTCTAATTTTCATTTTTTATTCAAATTAGTAATTAGTACTAATTTATTTTAA‑AAAAAAAAAAAAAAAAGTACATTAATTATTCa                                                                                                                          <  4:258644/148‑1 (MQ=255)
                          aTTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTCTTCTCCTTAGTAATTAGTACTAATTTCTTTTTATGACTGACT‑TAAAAAAGTACATTAATTATCCATCAACtat                                                                                                                  >  4:164354/1‑148 (MQ=255)
                                 aCTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGAtc                                                                                                           >  4:30092/1‑148 (MQ=255)
                                 aCTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATACATTAACtat                                                                                                                  >  1:34835/1‑141 (MQ=255)
                                    aGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGAtcttc                                                                                                        <  3:179561/148‑1 (MQ=255)
                                    aGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAAAtcttc                                                                                                        >  4:133286/1‑148 (MQ=255)
                                    aGTGGNGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGAATTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑NAAAAAAGTACATTAATTATTCATTAACTATATAGAtcttc                                                                                                        <  3:72797/148‑1 (MQ=255)
                                     gtggtgATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGAtcttct                                                                                                       >  3:20604/1‑148 (MQ=255)
                                          taTGCTAAAACTATTGCTAAAGTGCCCTCAATTATAGATTTTCTAATTTTCATTTTTTAGTCGCCTTAGGAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCttatta                                                                                                  <  3:331272/147‑1 (MQ=255)
                                          gATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGTAT‑ATAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCttatta                                                                                                  <  3:303871/148‑1 (MQ=255)
                                          gATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCttatta                                                                                                  <  3:166801/148‑1 (MQ=255)
                                                    cGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAAtt                                                                                        <  4:163047/148‑1 (MQ=255)
                                                        tGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATtaata                                                                                    <  4:196097/148‑1 (MQ=255)
                                                         gCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATtaataa                                                                                   >  4:395835/1‑148 (MQ=255)
                                                           tAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTACAGAGCTCCTTGTATGAAATGTAAATTAATAAAt                                                                                 >  4:187512/1‑148 (MQ=255)
                                                                    cGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAAtt                                                                        <  3:90470/148‑1 (MQ=255)
                                                                    cGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAAtt                                                                        <  3:312170/148‑1 (MQ=255)
                                                                    cGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAAtt                                                                        <  3:1579/148‑1 (MQ=255)
                                                                                 tttCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTAtt                                                           <  3:219589/148‑1 (MQ=255)
                                                                                         tttCATTTTTTTTTTTTTTTTGTAATTAGAACAAATTTATTTTAATTACTGACT‑AAAACAAGTAAATAAATTATTCATTAACTATATAGATTTTCTTATTAAATTAAAATTAATAAATTATAAAATTTACATATTTTATTGTAttttt                                                   >  4:84315/1‑146 (MQ=255)
                                                                                                          cTTAGTAATTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAgg                                  >  4:127286/1‑148 (MQ=255)
                                                                                                                aaTTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCa                            >  3:361092/1‑148 (MQ=255)
                                                                                                                aaTTAGTACTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCa                            >  4:79416/1‑148 (MQ=255)
                                                                                                                       aCTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATCGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATATATAGAAAAACAAAAAAAGGTAAGAACCGAAAt                     >  4:135256/1‑148 (MQ=255)
                                                                                                                       aCTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAAt                     >  4:392484/1‑148 (MQ=255)
                                                                                                                        cTAATTTATTTTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATg                    >  4:250521/1‑148 (MQ=255)
                                                                                                                           atttatttTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCtt                 >  3:185256/1‑148 (MQ=255)
                                                                                                                           atttatttTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCtt                 <  3:337822/148‑1 (MQ=255)
                                                                                                                              tatttTAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAAt                     >  1:11642/1‑141 (MQ=255)
                                                                                                                                  ttAATGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACt          >  4:137581/1‑148 (MQ=255)
                                                                                                                                    aaTGACTGACT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTAc               <  2:8102/141‑1 (MQ=255)
                                                                                                                                      tgactgacT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTccc      <  3:274375/148‑1 (MQ=255)
                                                                                                                                      tgactgacT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTccc      >  4:98366/1‑148 (MQ=255)
                                                                                                                                      tgactgacT‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCCTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTccc      >  4:358354/1‑148 (MQ=255)
                                                                                                                                         ctgact‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGATTACCTACt          >  2:47821/1‑141 (MQ=255)
                                                                                                                                          tgact‑AAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATaa  <  3:30092/148‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                               
CTAGCTTGTGCCTCATTTTTATCTAGATTAGTTACTAGTGGTGATGCTAAAACGATTGCTAAAGTTCCCGCAAGTATAGATTTTCTAATTTTCATTTTTTATTCTCCTTAGTAATTAGTACTAATTTATTTTAATGACTGACTAAAAAAAAGTACATTAATTATTCATTAACTATATAGATCTTCTTATTAAATGAAAATTAATAAATTATCAAATTGACATACCTTATTGTATTTATAGAAAAACAAAAAAAGGTAAGCACCGAAATGCTTACCTACTTCCCATAA  >  USA300TCH1516_ALE/2086755‑2087041

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: ‑

GATK/CNVnator alignment

N/A