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
A15 F55 I0 R1 245 145.6 7293262 93.0% 6782733 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,946,689 G→A 33.8% intergenic (+82/‑11) rrlC → / → rrfC 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,946,6890GA33.8% 258.9 / 239.4 260intergenic (+82/‑11)rrlC/rrfC23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon
Reads supporting (aligned to +/- strand):  ref base G (102/70);  new base A (82/6);  total (184/76)
Fisher's exact test for biased strand distribution p-value = 1.53e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.74e-02

Only 100 of 279 total aligned reads displayed.

ACCGTGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCT  >  NC_000913/3946590‑3946788
                                                                                                   |                                                                                                   
aCCGTGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatg                                                                                                     <  2:902534/100‑1 (MQ=35)
 ccGTGAGGCTTAACCTTACAACGCCTAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatg                                                                                                     <  1:3076981/99‑1 (MQ=18)
 ccGTGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatga                                                                                                    >  1:3281716/1‑100 (MQ=35)
  cGTGAGGCTTAACCTTACAACGCGGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatga                                                                                                    <  2:3446904/99‑1 (MQ=25)
  cGTGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaa                                                                                                   >  2:1663812/1‑100 (MQ=38)
  cGTGAGGCTTAACCTTACAACGCCGAAGATGTTCTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaa                                                                                                   >  2:2372777/1‑100 (MQ=38)
   gTGAGGCTTCACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATGAAATCAGAACGCAGAAGCGGTCTGATGaaa                                                                                                  >  2:1576280/1‑100 (MQ=255)
    tGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAAc                                                                                                 <  1:393708/100‑1 (MQ=38)
    tGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAAc                                                                                                 <  2:2836302/100‑1 (MQ=35)
    gtttcacttctgagttcggcatggggtcaggtgggaccaccgcgctactgccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAAc                                                                                                 >  1:1396239‑M1/72‑100 (MQ=255)
    gtttcacttctgagttcggcatggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAAc                                                                                                 >  2:2605364‑M1/72‑100 (MQ=255)
     tttcacttctgagttcggcatggggtcaggtgggaccaccgcgctactgccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAAc                                                                                                 >  2:1387407‑M1/71‑99 (MQ=255)
     tttcacttctgagttcggcatggggtcaggtgggaccaccgcgctactgccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAACa                                                                                                >  1:2486449‑M1/71‑100 (MQ=255)
     tttcacttctgagttcggcatggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAACa                                                                                                >  1:1351857‑M1/71‑100 (MQ=255)
     tttcacttctgagttcggcatggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAACa                                                                                                >  1:1967175‑M1/71‑100 (MQ=255)
     tttcacttctgagttcggcatggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAACa                                                                                                >  2:3388249‑M1/71‑100 (MQ=255)
      ttcacttctgagttcggcagggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAACAg                                                                                               >  1:66870‑M1/70‑100 (MQ=255)
      aGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAg                                                                                               >  2:3016143/1‑100 (MQ=35)
       tcacttctgagtggggcagggggtcaggtgggaccaccgcgctacgggcgccaggcaaattctgtttcATCAGAACGCAGAAGCGGTCTGATGAAACa                                                                                                >  2:3077834‑M1/69‑98 (MQ=255)
        cacttctgagttcggcatggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAACAGaa                                                                                             >  2:1554219‑M1/68‑100 (MQ=255)
         acttctgagttcggcatggggtcaggtgggaccaccgcgctacggccgccaggcaaattctgtttcATCAGAACGCAGAAGCGGTCTGATGAAACAGAAt                                                                                            >  2:1997369‑M1/67‑100 (MQ=255)
            aaCCTTACGACGCCGAAGATGTTTTGCCCGATGAGAGAAGCTTTTCAGCCTGATACAGCTTAACTCACCACCCAGAAGCGGGCTGCTGGAACAGAATTTg                                                                                         >  2:139110/1‑100 (MQ=11)
            aaCCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTg                                                                                         <  1:2544401/100‑1 (MQ=38)
              tgagttcggcatggggtcaggtgggaccaccgcgctactgccgccaggcaaattctgttttATCAGAACGCAGAAGCGGTCTGATAAAAcagaatagatc                                                                                       <  2:974691‑M1/39‑6 (MQ=255)
                ttACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTg                                                                                     <  1:2767347/100‑1 (MQ=38)
                  ncAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggc                                                                                   >  2:2518856/2‑100 (MQ=38)
                   cAACGCCGAAGTTGTTTTGTTGGATGAGAGAATATTTTCAGCGTGATACAGATTAAATCACAACGGAGAAGAGGTCTGATGAAACATAATTTGcgt                                                                                      >  2:1202742/1‑94 (MQ=11)
                    aaCGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACTCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg                                                                                 <  1:2565150/100‑1 (MQ=255)
                        ccGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGt                                                                             >  2:2801149/1‑100 (MQ=38)
                          gAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAg                                                                           <  2:1914783/100‑1 (MQ=38)
                           aaGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGCCTGATGAAACAGAATTTGCCTGGCGGCCGTCgc                                                                          >  2:1568470/1‑100 (MQ=255)
                              aTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGcgcg                                                                       <  2:18937/100‑1 (MQ=35)
                              aTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGcgcg                                                                       >  1:1024429/1‑100 (MQ=35)
                              aTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGcgcg                                                                       >  2:1638221/1‑100 (MQ=35)
                               tGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTAGCGGCCGTAGCGCgg                                                                      <  1:521869/100‑1 (MQ=18)
                                     ggCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTcc                                                                >  1:802344/1‑100 (MQ=33)
                                       nggATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCa                                                              >  1:2054033/2‑100 (MQ=18)
                                       cGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCa                                                              <  1:1747166/100‑1 (MQ=33)
                                        ggATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCAc                                                             >  1:2310240/1‑100 (MQ=33)
                                                naagaTTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGAcccc                                                     >  1:3240328/2‑100 (MQ=18)
                                                 aagaTTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCa                                                    <  1:1134419/100‑1 (MQ=33)
                                                     ttttCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGcc                                                <  1:3510556/100‑1 (MQ=33)
                                                     ttttCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGcc                                                <  1:319942/100‑1 (MQ=32)
                                                     ttttCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGc                                                 <  1:3356559/99‑1 (MQ=32)
                                                       ttCAGCCTGATACAGATTAAATCAGAACGCAGCAGCGGTCTGATGAAACAGAATTTGCTTGACGGCCGTAGCGCGGTGCTCCCACCGGCCCCCATgacta                                              >  1:3038110/1‑96 (MQ=11)
                                                       ttCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGa                                              >  2:2695288/1‑100 (MQ=33)
                                                           gCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTc                                          >  2:603406/1‑100 (MQ=33)
                                                            ccTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCa                                         <  1:612227/100‑1 (MQ=33)
                                                             tccgatcttgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAg                                        <  1:804995‑M2/62‑1 (MQ=255)
                                                             cTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAg                                        <  2:1837368/100‑1 (MQ=33)
                                                               gATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGaa                                      >  1:2816990/1‑100 (MQ=33)
                                                                aTACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAg                                     <  2:2997575/100‑1 (MQ=33)
                                                                 tACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGt                                    >  1:1592047/1‑100 (MQ=32)
                                                                   tctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGa                                  >  1:2606904‑M2/33‑100 (MQ=255)
                                                                   cAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGa                                  <  1:2631785/100‑1 (MQ=33)
                                                                   cAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGa                                  <  1:1817397/100‑1 (MQ=33)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  1:1493263‑M2/32‑100 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  1:1475763‑M2/32‑100 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  1:693096‑M2/32‑100 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  1:548976‑M2/32‑100 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 <  2:1493255‑M2/69‑1 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  1:1286954‑M2/32‑100 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  1:3412086‑M2/32‑100 (MQ=255)
                                                                    ctgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 >  2:1754273‑M2/32‑100 (MQ=255)
                                                                    aGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 <  1:2332972/100‑1 (MQ=33)
                                                                    aGATTAAATCAGAACGCAGAAGAGAGCTGATGAAACACAAGTCGCCTGGCGGCCGGAGCGGGGAGGTCCCACCTGCCCCCATGCCGAATTCAGAAGTg                                   <  2:2427920/98‑1 (MQ=11)
                                                                     tgttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaaa                                >  2:3389232‑M2/31‑100 (MQ=255)
                                                                     cttccgATCTGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaaa                                >  1:1365908‑M1/7‑100 (MQ=255)
                                                                      nttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:1408253‑M2/30‑100 (MQ=255)
                                                                      gttttattagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:1918414‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:2964835‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:2735726‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:1178110‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  2:1930940‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:2172575‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:341285‑M2/30‑100 (MQ=255)
                                                                      gttttatcagaccgcttctgcgttctgatAAAAAAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACATGACCCCATGCCGAACTCAGAAGTGAAAc                               >  2:2188718‑M2/30‑100 (MQ=255)
                                                                      gtttcATCAGATCGCTTCTGCGTTCTGATGAAACAGAATTTGCCTGCCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGaa                                 <  2:1902684‑M1/93‑1 (MQ=255)
                                                                      aTTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAAc                               >  1:989542/1‑100 (MQ=33)
                                                                       ttttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACg                              >  1:2140425‑M2/29‑100 (MQ=255)
                                                                        tttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGc                             >  2:3055590‑M2/28‑100 (MQ=255)
                                                                        tttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGc                             >  1:2375129‑M2/28‑100 (MQ=255)
                                                                         ttatcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGcc                            >  1:846529‑M2/27‑100 (MQ=255)
                                                                         tcatcagaccgcttctgcgttctgatGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGcc                            >  1:964029‑M2/27‑100 (MQ=255)
                                                                         aaaTCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGcc                            >  2:2157545/1‑100 (MQ=32)
                                                                          aaTCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCg                           <  2:2726230/100‑1 (MQ=32)
                                                                           atcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGt                          >  2:1342789‑M2/25‑100 (MQ=255)
                                                                            tcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTa                         >  2:2658651‑M2/24‑100 (MQ=255)
                                                                            tcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTa                         >  2:1244153‑M2/24‑100 (MQ=255)
                                                                            tcagaccgcttctgcgttctgatAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTa                         >  2:3498107‑M2/24‑100 (MQ=255)
                                                                              AGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAgc                       <  2:1284862‑M1/100‑1 (MQ=255)
                                                                              AGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAgc                       >  1:1108640‑M1/1‑100 (MQ=255)
                                                                                    cAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGAt                 >  2:3227331/1‑100 (MQ=32)
                                                                                      gAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATgg               <  2:3314780/100‑1 (MQ=33)
                                                                                      gAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATgg               >  2:473914/1‑100 (MQ=33)
                                                                                        aGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTa             <  2:2024627/100‑1 (MQ=32)
                                                                                           ggTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAgtg          >  1:289786/1‑100 (MQ=33)
                                                                                                gatGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTgggg     >  2:1807333‑M2/4‑100 (MQ=255)
                                                                                                gatGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTgggg     <  2:1116330‑M2/97‑1 (MQ=255)
                                                                                                  tGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTc   >  2:426771‑M2/2‑100 (MQ=255)
                                                                                                   |                                                                                                   
ACCGTGAGGCTTAACCTTACAACGCCGAAGATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCT  >  NC_000913/3946590‑3946788

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