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
A19 F74 I1 R1 14 98.0 2279172 93.9% 2140142 133.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,319,519 G→A Q152* (CAA→TAA)  USA300HOU_RS11830 ← Alkaline shock protein 23

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,319,5190GA97.8% 312.5 / NA 92Q152* (CAA→TAA) USA300HOU_RS11830Alkaline shock protein 23
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (37/53);  minor base T (2/0);  total (39/53)
Fisher's exact test for biased strand distribution p-value = 1.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTGTTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCTGATTCACCAT  >  USA300TCH1516_ALE/2319382‑2319653
                                                                                                                                         |                                                                                                                                      
tttCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTAttt                                                                                                                                     >  3:325049/1‑141 (MQ=255)
tttCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTAttt                                                                                                                                     >  3:324995/1‑141 (MQ=255)
 ttCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTc                                                                                                                                    >  1:327418/1‑141 (MQ=255)
  tCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTcc                                                                                                                                   <  3:280378/141‑1 (MQ=255)
   cTATCAAATAATTAATAGAAATCAGCTTTTTTTTTTTTTTTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTTTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTAttttta                                                                                                                                  >  2:345277/1‑138 (MQ=37)
    tATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCAc                                                                                                                                 <  3:38513/141‑1 (MQ=255)
    tATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCAc                                                                                                                                 >  3:320441/1‑141 (MQ=255)
    tATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCAc                                                                                                                                 <  2:510683/141‑1 (MQ=255)
    tATCAAANAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCAc                                                                                                                                 <  2:594143/141‑1 (MQ=255)
       cAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCActct                                                                                                                              <  1:79716/141‑1 (MQ=255)
       cAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCACTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCActct                                                                                                                              <  1:358040/141‑1 (MQ=255)
        aaaTAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAATCCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCtt                                                                                                                             <  4:269095/141‑1 (MQ=255)
            aattaatAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCtttttt                                                                                                                         >  2:509683/1‑140 (MQ=255)
               taatAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGt                                                                                                                      <  4:89822/141‑1 (MQ=255)
               taatAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGt                                                                                                                      <  1:301556/141‑1 (MQ=255)
                 atAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCa                                                                                                                    <  1:763940/141‑1 (MQ=255)
                  tAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTcc                                                                                                                                   <  4:289332/125‑1 (MQ=255)
                  tAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTAATTTcc                                                                                                                                   >  3:289332/1‑125 (MQ=255)
                    gAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGTGTCATTa                                                                                                                 >  2:602894/1‑141 (MQ=255)
                         cAGCTTTTTTACATTTCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCg                                                                                                            >  4:21636/1‑141 (MQ=255)
                         cAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCg                                                                                                            <  2:772254/141‑1 (MQ=255)
                           gCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTc                                                                                                          <  2:407074/141‑1 (MQ=255)
                           gCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTc                                                                                                          <  2:131186/141‑1 (MQ=255)
                            cTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGCGTCATTACATCGTCa                                                                                                         >  2:334887/1‑141 (MQ=255)
                            cTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCa                                                                                                         >  1:374010/1‑141 (MQ=255)
                              tttttACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCAt                                                                                                                   <  4:10346/129‑1 (MQ=255)
                              tttttACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCAt                                                                                                                   >  3:10346/1‑129 (MQ=255)
                                 ttACATTNCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCTACTTg                                                                                                    <  2:595234/141‑1 (MQ=255)
                                 ttACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTg                                                                                                    <  3:23198/141‑1 (MQ=255)
                                      ttGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTTTTTTTGAGTCATTACATCGTCAACTTGCATGt                                                                                               >  2:300904/1‑141 (MQ=255)
                                      ttGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGt                                                                                               >  3:190285/1‑141 (MQ=255)
                                         ccTAAGAATTTAATGTCCCAAGCCCTTTTTATCGTATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTaa                                                                                            >  4:200280/1‑141 (MQ=255)
                                          cTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAAc                                                                                           <  2:78176/141‑1 (MQ=255)
                                          cTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAAc                                                                                           <  2:255601/141‑1 (MQ=255)
                                            aaGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACtt                                                                                         <  1:417579/141‑1 (MQ=255)
                                            aaGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACtt                                                                                         <  2:370350/141‑1 (MQ=255)
                                             aGAATTTAATGTCCCAAGCCCTTTTTATCTATTAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGGTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTc                                                                                        <  2:166681/141‑1 (MQ=255)
                                                aTTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACt                                                                                                      <  1:325800/124‑1 (MQ=255)
                                                aTTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACt                                                                                                      >  2:325800/1‑124 (MQ=255)
                                                  ttAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCAc                                                                                                                                 <  1:329166/95‑1 (MQ=255)
                                                  ttAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCAc                                                                                                                                 >  2:329166/1‑95 (MQ=255)
                                                  ttAATGTCCCAAGCCCTTTTTATCGAATAACTTATTATAAACCTGTGCTTTCTTGATTATGCGTTTCTTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTa                                                                                   <  1:472337/141‑1 (MQ=255)
                                                  ttAATGTCCCAAGCCCTTCTTATCGAATAACTTATTGTAAACCTTGTCTTTATTGGTTATTGTTTTCGTTATTTTTTTCTTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCTTCAACTTGCATGTTAACTTCAACTa                                                                                   >  3:267265/1‑141 (MQ=255)
                                                   tAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTTAGTCATTTCATCGTCAACTTGCATGTTAACTTCAACTAc                                                                                  >  4:313322/1‑141 (MQ=255)
                                                    aaTGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACa                                                                                 <  4:320441/141‑1 (MQ=255)
                                                    aaTGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACa                                                                                 >  4:205766/1‑141 (MQ=255)
                                                     aTGTCCCAAGCCCTTTTTATCGAATAACTTATTTTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACAt                                                                                >  1:186230/1‑141 (MQ=255)
                                                     aTGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCATTCTTGGTTCTTGTTTTCATACTTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACAt                                                                                <  1:234209/141‑1 (MQ=255)
                                                          ccAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTaaa                                                                           >  1:756047/1‑141 (MQ=255)
                                                           cAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAAc                                                                          <  3:200798/141‑1 (MQ=255)
                                                            aaGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAAcc                                                                         <  1:532308/141‑1 (MQ=255)
                                                             aGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCa                                                                        <  3:279717/141‑1 (MQ=255)
                                                                 cTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTaa                                                                    <  1:345277/141‑1 (MQ=255)
                                                                 cTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACATGCATGTTAACTTCAACTACATCTAAACCAGTaa                                                                    >  3:186211/1‑141 (MQ=255)
                                                                  tttttATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTTTTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAat                                                                   >  2:438594/1‑141 (MQ=255)
                                                                      tATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAatatat                                                               >  2:509625/1‑141 (MQ=255)
                                                                       aTCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATAtt                                                              <  4:324995/141‑1 (MQ=255)
                                                                       aTCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATAtt                                                              <  4:325049/141‑1 (MQ=255)
                                                                        tCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTa                                                                             <  4:213681/125‑1 (MQ=255)
                                                                        tCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTa                                                                             >  3:213681/1‑125 (MQ=255)
                                                                        tCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATAttt                                                             >  1:570308/1‑141 (MQ=255)
                                                                          gAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTaa                                                           <  2:174121/141‑1 (MQ=255)
                                                                          gAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAAACAGTAATAAATTTag                                                           >  1:126543/1‑140 (MQ=255)
                                                                             tAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACtt                                                        <  2:414429/141‑1 (MQ=255)
                                                                             tAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACtt                                                        <  2:722151/141‑1 (MQ=255)
                                                                              aaCTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTg                                                       <  1:143916/141‑1 (MQ=255)
                                                                               aCTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGt                                                      <  1:613112/141‑1 (MQ=255)
                                                                               aCTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGt                                                      <  1:286249/141‑1 (MQ=255)
                                                                                 ttATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTc                                                    <  2:301937/141‑1 (MQ=255)
                                                                                       tAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAAc                                              <  1:509683/141‑1 (MQ=255)
                                                                                         aaCCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTa                                            >  2:729791/1‑141 (MQ=255)
                                                                                           ccTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAAt                                          >  3:87613/1‑141 (MQ=255)
                                                                                               gTCTTTCTTGGTTATTGTTTTCGTTGTTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACTTCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATGCAg                                      <  2:327418/141‑1 (MQ=255)
                                                                                                tctttcttGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTTCACTCTTTTTGAGTAATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGt                                     >  2:339141/1‑141 (MQ=255)
                                                                                                   ttcttGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTAc                                  <  3:21636/141‑1 (MQ=255)
                                                                                                     cttGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCaa                                                                                                        <  4:81745/69‑1 (MQ=255)
                                                                                                     cttGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCaa                                                                                                        >  3:81745/1‑69 (MQ=255)
                                                                                                          ttATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACgg                           <  1:509625/141‑1 (MQ=255)
                                                                                                          ttATTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACgg                           <  2:649248/141‑1 (MQ=255)
                                                                                                            aTTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGaa                         >  3:334575/1‑141 (MQ=255)
                                                                                                            aTTGTTTTCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGaa                         <  2:242440/141‑1 (MQ=255)
                                                                                                                ttttCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGAtt                     <  1:729791/141‑1 (MQ=255)
                                                                                                                  ttCGTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTTTTTATATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGAtttt                   >  2:81075/1‑141 (MQ=255)
                                                                                                                     gTTATTTTTTTCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTgg                >  1:10489/1‑141 (MQ=255)
                                                                                                                       tATTTTTTTCTTTTTTTTTTTTCCACTCTTTTTGAGTCATTATATCGTCAACTTTCATGTTAACTTCAACTACTTCTAAACCAGTAATATATTTAACTTTTTCTTTATCTTTTTTATTTACTTTACGTAAGAttttttttt              >  2:173969/1‑137 (MQ=255)
                                                                                                                         tttttttCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTACATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCt            >  1:89696/1‑141 (MQ=255)
                                                                                                                         tttttttCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTACATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCt            >  1:89686/1‑141 (MQ=255)
                                                                                                                         tttttttCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACATGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCt            <  4:186211/141‑1 (MQ=255)
                                                                                                                          ttttttCGTGTTTTTATTTCCTCTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCTg           <  2:315127/141‑1 (MQ=255)
                                                                                                                               tCGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCTGATTCa      >  3:196269/1‑141 (MQ=255)
                                                                                                                                cGTGTTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTCCCCTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCTGATTCAc     <  3:283529/141‑1 (MQ=255)
                                                                                                                                   gtTTTTATTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCTGATTCACCat  <  4:156070/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                      
TTTCTATCAAATAATTAATAGAAATCAGCTTTTTTACATTGCCTAAGAATTTAATGTCCCAAGCCCTTTTTATCGAATAACTTATTGTAAACCTTGTCTTTCTTGGTTATTGTTTTCGTTATTTTTTTCGTGTTTTTGTTTCCACTCTTTTTGAGTCATTACATCGTCAACTTGCATGTTAACTTCAACTACATCTAAACCAGTAATATATTTAACTTGTTCTTTAACTAATTCAGTTACTTTACGGAAGATTTTTGGTGCTGATTCACCAT  >  USA300TCH1516_ALE/2319382‑2319653

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: ‑

GATK/CNVnator alignment

N/A