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
A4 F53 I0 R1 47 135.3 6511354 96.7% 6296479 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 107,553 (T)9→8 100% intergenic (+79/‑152) lpxC → / → secM UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913107,5450T.96.2% 568.0 / 14.5 130intergenic (+71/‑160)lpxC/secMUDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation
Reads supporting (aligned to +/- strand):  ref base T (4/1);  new base . (67/58);  total (71/59)
Fisher's exact test for biased strand distribution p-value = 3.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 142 total aligned reads displayed.

CAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAC  >  NC_000913/107447‑107640
                                                                                                   |                                                                                               
cAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtt                                                                                                <  1:2320388/100‑1 (MQ=255)
 aaaGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttt                                                                                               >  2:970920/1‑100 (MQ=255)
  aaGCGCCTTCAGCTGTACTGGTATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGTCACTCTCTCCGGCCAGGTGAACCAGTCGtttt                                                                                              <  2:610148/100‑1 (MQ=255)
    gcgcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtttttt                                                                                            >  1:3003271/1‑100 (MQ=255)
      gcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtttttttt                                                                                          <  2:1747397/100‑1 (MQ=255)
       ccTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttg                                                                                         <  1:2177320/100‑2 (MQ=255)
         ttCAGCTGTACTGGCATAACGACATTAATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCGCCGGCCAGGTGAACCAGTCGttttttttga                                                                                        >  2:353202/1‑97 (MQ=255)
           cAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAAtt                                                                                    >  2:2798396/1‑100 (MQ=255)
            agttGTACTGGCATAACGACATTTATATTGTCTTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTTAACCAGTCG‑TTTTTTTTGAAttt                                                                                   <  2:780676/97‑1 (MQ=255)
             gCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAAtttt                                                                                  <  2:126536/100‑1 (MQ=255)
               tGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTtat                                                                                <  2:195321/100‑1 (MQ=255)
               tGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTtat                                                                                <  2:296180/100‑1 (MQ=255)
                gTACTGGCATAACGACATTTATAATGTCGTATAAAATTCGACTGGC‑AAATCTGGCAATCTCTCCGGCTAGGAGAAGCAGTCG‑TTTTTTTTGAATTTtat                                                                                >  2:666977/1‑99 (MQ=255)
                 tACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATaa                                                                              >  2:2628258/1‑100 (MQ=255)
                  aCTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAag                                                                             <  2:2234279/100‑1 (MQ=255)
                   cTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAaga                                                                            >  1:3115967/1‑100 (MQ=255)
                   cTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAaga                                                                            >  1:1022370/1‑100 (MQ=255)
                     ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                          <  2:687825/100‑1 (MQ=255)
                     ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                          <  1:314088/100‑1 (MQ=255)
                     ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                          >  2:249325/1‑100 (MQ=255)
                       cttAACGACATTTATACTGTTGTATAAAATTCCACTGGC‑AAATCTAGCACTCTCTGCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCta                                                                        <  1:2718157/98‑1 (MQ=255)
                       cATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCta                                                                        >  2:1351253/1‑100 (MQ=255)
                        aTAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCtat                                                                       >  1:859588/1‑100 (MQ=255)
                           aCGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATaaa                                                                    >  1:3165725/1‑100 (MQ=255)
                              aCATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATaaaaaa                                                                 >  2:2294647/1‑100 (MQ=255)
                               cATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAAc                                                                >  2:67901/1‑100 (MQ=255)
                                 tttATCCGGTCGAATAAAATT‑GGCTGGCAAAATTTGCAATTTTCTCCGGCAAGTGGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACgg                                                              <  2:2304657/100‑1 (MQ=255)
                                 tttATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACgg                                                              <  1:2453482/100‑1 (MQ=255)
                                  ttATACTGTCGTATAAAATTCGACTGGC‑AAATATGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACgg                                                              >  2:2600267/1‑99 (MQ=255)
                                    ataCTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGc                                                           <  2:2365049/100‑1 (MQ=255)
                                    ataCTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGc                                                           <  1:2016324/100‑1 (MQ=255)
                                     taCTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCg                                                          >  1:2155396/1‑100 (MQ=255)
                                      aCTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCTGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAAAACTATAAAAAACGGTGCg                                                          <  2:387978/99‑1 (MQ=255)
                                         gTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACg                                                      <  2:1194339/100‑1 (MQ=255)
                                            gTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGTCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTg                                                   >  2:1742428/1‑100 (MQ=255)
                                            gTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTg                                                   >  1:2780583/1‑100 (MQ=255)
                                            gTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTg                                                   >  1:2624876/1‑100 (MQ=255)
                                             tataAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGt                                                  <  2:2214887/100‑1 (MQ=255)
                                             tataAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGt                                                  >  1:2476157/1‑100 (MQ=255)
                                             tataAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGt                                                  >  1:2564193/1‑100 (MQ=255)
                                              ataAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTT‑TATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGtt                                                 >  2:2053524/1‑100 (MQ=255)
                                               taAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGagatcggaag                                                >  1:2215569/1‑91 (MQ=255)
                                               taAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGttt                                                >  2:251501/1‑100 (MQ=255)
                                                 tctttCGACGGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                              <  1:1009139/97‑1 (MQ=255)
                                                 aaaTTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGtttt                                               >  2:2761962/1‑99 (MQ=255)
                                                  aaTTCGACTGGC‑AGATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                              <  2:2758970/99‑1 (MQ=255)
                                                  aaTTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCt                                             <  1:190890/100‑1 (MQ=255)
                                                  aaTTCGAAGGGC‑AAATCTGGCACTCTCTCCGACCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTAAAAAAAAAAAAAAAAACGGTGCGAACGCTGTTTTCt                                             <  2:898247/100‑1 (MQ=255)
                                                    ttCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTcaga                                           >  2:1009134/1‑97 (MQ=255)
                                                    ttCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTa                                           <  1:1018361/100‑1 (MQ=255)
                                                    ttCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTa                                           >  1:2999745/1‑100 (MQ=255)
                                                    ttCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTC‑TTTTTTTTTTAATTTTATAAGAGCTATAAAAAACAGTGCGAACGCTGTTTTCTTa                                           >  1:1133764/1‑100 (MQ=255)
                                                     tCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTaa                                          <  1:2838164/100‑1 (MQ=255)
                                                      cGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                         >  2:2706386/1‑100 (MQ=255)
                                                       gACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGc                                        >  1:786745/1‑100 (MQ=255)
                                                       gACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAAAAAAAAAAAAAACGGTGCGAACGCTGTTTTCTTAAGc                                        <  2:2439603/100‑1 (MQ=255)
                                                        aCTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAACa                                       >  1:2071/1‑100 (MQ=255)
                                                         cTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                      <  2:209912/100‑1 (MQ=255)
                                                         cTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                      >  1:1903952/1‑100 (MQ=255)
                                                         cTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                      >  2:1946875/1‑100 (MQ=255)
                                                          tGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACt                                     <  2:2041760/100‑1 (MQ=255)
                                                          tGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGAGAACGCTGTTTTCTTAAGCAc                                      >  2:405036/1‑99 (MQ=255)
                                                          tGGC‑AAATCTGGCACTATCTCCGGCCAGGTGAACCAGTAG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACt                                     <  1:2336027/100‑1 (MQ=255)
                                                           ggC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  2:2508977/1‑100 (MQ=255)
                                                           ggC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  1:1441667/1‑100 (MQ=255)
                                                           ggC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  1:1771685/1‑100 (MQ=255)
                                                           ggC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  1:831023/1‑100 (MQ=255)
                                                           ggC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  2:2720850/1‑100 (MQ=255)
                                                            gC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACttt                                   <  2:2389145/100‑1 (MQ=255)
                                                             c‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATACAAAACGGTGCGAACGCTGTTTTCTTAAGCACtttt                                  >  1:2854147/1‑100 (MQ=255)
                                                               aaaTCTTGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTc                                 <  1:3027087/100‑1 (MQ=255)
                                                               aaaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtttt                                  >  1:2523625/1‑99 (MQ=255)
                                                               aaaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTc                                 >  1:712022/1‑100 (MQ=255)
                                                               aaaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTc                                 >  1:2523495/1‑100 (MQ=255)
                                                                aaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTcc                                >  2:2415718/1‑100 (MQ=255)
                                                                aaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTcc                                <  2:1110560/100‑1 (MQ=255)
                                                                    tGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcac                            <  2:1412580/100‑1 (MQ=255)
                                                                    tGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcac                            <  2:1158185/100‑1 (MQ=255)
                                                                      gctctctctCCGGCCAGGTGAACAAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcac                            <  1:2756580/95‑1 (MQ=255)
                                                                      gCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACaa                          >  1:1417992/1‑100 (MQ=255)
                                                                         ctctctCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACaagat                       >  2:2553977/1‑97 (MQ=255)
                                                                            tctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCGATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATc                    >  2:2592487/1‑100 (MQ=255)
                                                                             ctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCt                   >  1:1688217/1‑100 (MQ=255)
                                                                              tcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCt                   >  1:1578775/1‑99 (MQ=255)
                                                                               ccGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTc                 <  2:1130032/100‑1 (MQ=255)
                                                                                ctgCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCa                <  1:1129184/98‑1 (MQ=255)
                                                                                    cAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTc             <  2:790260/100‑1 (MQ=255)
                                                                                    cAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCg            <  1:733360/100‑1 (MQ=255)
                                                                                     aGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGt           >  2:2175533/1‑100 (MQ=255)
                                                                                      ggTGAACCAGTCGTTTTTTTTT‑TTTTTTTTTAGTGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACACCTTATCTTCATTCGt           >  1:1399739/1‑99 (MQ=255)
                                                                                          aaCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtgt      <  2:3048187/100‑1 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGATCGCTGTTTTCTTAAGCACTTTTCCGCACAACTGATCTTCATTCGTGCtgtn     <  2:1548213/100‑2 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtgtg     <  1:2628279/100‑1 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtgtg     <  1:3004812/100‑1 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtgtg     <  1:740899/100‑1 (MQ=255)
                                                                                            ccAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTgg    <  1:249327/100‑1 (MQ=255)
                                                                                            ccAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTgg    <  1:1171326/100‑1 (MQ=255)
                                                                                             cAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTgg    >  1:1427004/1‑99 (MQ=255)
                                                                                              aGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAc  <  2:2523607/100‑1 (MQ=255)
                                                                                              aGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAc  <  1:2600674/100‑1 (MQ=255)
                                                                                                   |                                                                                               
CAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGC‑AAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAC  >  NC_000913/107447‑107640

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A