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
A16 F258 I0 R1 432 103.0 5191697 92.7% 4812703 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.93.8% 314.9 / 14.4 81intergenic (+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 . (40/36);  total (44/37)
Fisher's exact test for biased strand distribution p-value = 3.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.27e-01

TCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGA  >  NC_000913/107446‑107639
                                                                                                   |                                                                                              
tCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGt                                                                                                >  2:825683/1‑100 (MQ=255)
tCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGt                                                                                                <  2:1553289/100‑1 (MQ=255)
tCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGt                                                                                                <  2:943254/100‑1 (MQ=255)
 cAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCCTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtt                                                                                               <  2:269627/100‑1 (MQ=255)
  aaaGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttt                                                                                              >  2:353152/1‑100 (MQ=255)
    aGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttt                                                                                            >  2:1960910/1‑100 (MQ=255)
     gcgcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtttttt                                                                                           >  2:747960/1‑100 (MQ=255)
     gcgcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtttttt                                                                                           <  2:1177082/100‑1 (MQ=255)
      cgcCTTCAGCTCTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttt                                                                                            <  2:110726/98‑1 (MQ=255)
        ccTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCTCTCTCTCCGGCCAGGTGAACCAGTCGttttttttt                                                                                        <  1:2239333/100‑1 (MQ=255)
        ccTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttg                                                                                        <  2:951575/100‑2 (MQ=255)
         cTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttga                                                                                       >  2:2234110/1‑98 (MQ=255)
              gCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCCGGTGAACCAGTCG‑TTTTTTTTGAAtttt                                                                                 >  2:775190/1‑100 (MQ=255)
              gCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAAtttt                                                                                 >  2:2304693/1‑100 (MQ=255)
                   aCTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAag                                                                            <  1:2507474/100‑1 (MQ=255)
                    cTGGCATAACGACATTTAGACTGGCGTATAAAATTGGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAag                                                                            <  1:458163/99‑1 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGATTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                         <  2:1818882/100‑1 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                         >  2:1850301/1‑100 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                         <  2:751124/100‑1 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                         <  2:415083/100‑1 (MQ=255)
                       gCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCt                                                                        <  2:241870/100‑1 (MQ=255)
                        cATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCta                                                                       >  2:1998982/1‑100 (MQ=255)
                            aCGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGACCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGAtata                                                                     >  1:1900394/1‑98 (MQ=255)
                             cGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATaaaa                                                                  <  2:1335591/100‑1 (MQ=255)
                                cATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTT‑TATTTTTTAAGAGCTATAAAAAAc                                                               >  1:68909/1‑100 (MQ=255)
                                cATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGTCTTTTATAATAGCTATAAAAAAc                                                               >  1:1269166/1‑100 (MQ=255)
                                cATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAAc                                                               >  2:142256/1‑100 (MQ=255)
                                cATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGGCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAAc                                                               >  1:2425089/1‑100 (MQ=255)
                                 aTTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAAc                                                               <  2:874893/99‑1 (MQ=255)
                                 aTTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACg                                                              <  2:76198/100‑1 (MQ=255)
                                   ttATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGt                                                            <  2:2011980/100‑1 (MQ=255)
                                     ataCTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTT‑TTTTTTTTTAGAGCTATAAAAAACGGTGc                                                          >  1:1468485/1‑100 (MQ=255)
                                     aaaatgaagTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTAAAAAAAAAAAAAAAAACgg                                                             <  1:2139081/89‑1 (MQ=255)
                                      taCTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCg                                                         >  2:343527/1‑100 (MQ=255)
                                        cTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGaa                                                       >  2:1927406/1‑100 (MQ=255)
                                        cTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGaa                                                       >  1:2065777/1‑100 (MQ=255)
                                        cTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGaa                                                       >  2:1641476/1‑100 (MQ=255)
                                         tGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAAc                                                      >  2:145963/1‑100 (MQ=255)
                                         tGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAAc                                                      <  2:415896/100‑1 (MQ=255)
                                          gTCGTATGAAATTCGTCTTGTAATTCTTTTACTCTCTCCGCGCACGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGTTGCGaa                                                       <  1:1258529/98‑1 (MQ=255)
                                             gTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGc                                                    <  2:2065790/98‑1 (MQ=255)
                                             gTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTg                                                  >  2:2322797/1‑100 (MQ=255)
                                               ataAAATTCGACTGGCAAATCTGACACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGtt                                                >  1:874863/1‑100 (MQ=255)
                                                taAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAATAGCTATAAAAAACGGTGCGAACGCTGttt                                               >  1:144396/1‑100 (MQ=255)
                                                taAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGttt                                               <  2:1836510/100‑1 (MQ=255)
                                                  aaaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                             >  2:1985184/1‑100 (MQ=255)
                                                  aaaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                             >  2:776873/1‑100 (MQ=255)
                                                  aaaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                             >  2:1652665/1‑100 (MQ=255)
                                                    aTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCtt                                           <  2:1513435/100‑1 (MQ=255)
                                                       cGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                        <  1:521818/100‑1 (MQ=255)
                                                       cGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                        >  2:2485959/1‑100 (MQ=255)
                                                        gACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGc                                       >  2:1836192/1‑100 (MQ=255)
                                                          cTGGCATATTTTGCATTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGATCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                     <  1:820197/100‑1 (MQ=255)
                                                          cTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                     >  2:67086/1‑100 (MQ=255)
                                                          cTGGCAAATCTGGCACTCTCTCCGGCCAGGGGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                     <  1:316667/100‑1 (MQ=255)
                                                           tGGCAAATCTGGCATTCTTTCCGGTCAGGTGGATTAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACTGTGCGAACGCTGTTTTCTTAAGc                                       <  1:1367442/97‑1 (MQ=255)
                                                           tGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACt                                    <  2:944945/100‑1 (MQ=255)
                                                             gCAAATCTGGCACTCCCTCCGGCCAGGTGAACCAGTCG‑‑TTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtttt                                 >  2:1059763/1‑100 (MQ=255)
                                                              cAAAACTGTCACTCTCCCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGATTTTTATAAAAAAAAAAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACttt                                  <  1:172393/99‑1 (MQ=255)
                                                               agaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAATAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTc                                >  2:1752696/3‑100 (MQ=255)
                                                               aaaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTc                                <  2:143574/100‑1 (MQ=255)
                                                                 aTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCg                              >  2:1189931/1‑100 (MQ=255)
                                                                 aTCTGGCACTCTCTCCCGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCg                              <  1:1516514/100‑1 (MQ=255)
                                                                  tCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGc                             <  1:879872/100‑1 (MQ=255)
                                                                   cTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGca                            >  2:2280931/1‑100 (MQ=255)
                                                                   cTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGca                            >  2:2280962/1‑100 (MQ=255)
                                                                    tGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcac                           <  1:1788189/100‑1 (MQ=255)
                                                                      gcccccgctcCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcaca                          <  2:819221/93‑1 (MQ=255)
                                                                        aCTCTCTCCGGCCAGGTGAACCAGTCG‑GTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcac                           <  1:338480/96‑1 (MQ=255)
                                                                          tctctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGATTTTTATAAGAACTATCAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAAc                        >  1:572351/1‑97 (MQ=255)
                                                                          tctctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTa                     >  2:2590339/1‑100 (MQ=255)
                                                                           ctctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTAt                    >  2:2390941/1‑100 (MQ=255)
                                                                            tctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATc                   <  1:1856911/100‑1 (MQ=255)
                                                                            tccccGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATc                   <  2:2345593/97‑1 (MQ=255)
                                                                             ctcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCt                  >  1:2376272/1‑100 (MQ=255)
                                                                              tcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCtt                 <  2:2210622/100‑1 (MQ=255)
                                                                              tcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCtt                 >  1:50807/1‑100 (MQ=255)
                                                                              tcCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAACCGCTTTTCCGCACAACTTATCtt                 >  1:785533/1‑100 (MQ=255)
                                                                               ccGGCCAGGTGAACCTGTCGTTTTTTTTT‑TTTTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTc                >  1:659911/1‑100 (MQ=255)
                                                                               ccGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTc                >  2:162167/1‑100 (MQ=255)
                                                                               ccGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTc                >  1:780439/1‑100 (MQ=255)
                                                                                cGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTc                >  2:2297216/1‑99 (MQ=255)
                                                                                    cAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCg           >  2:2040253/1‑100 (MQ=255)
                                                                                    cAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCg           <  1:1483931/100‑1 (MQ=255)
                                                                                    cAGGTGAACCAGTAG‑TTTTTTTTGAATTTTAAAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCg           >  2:1744070/1‑100 (MQ=255)
                                                                                      ggTGAACCAGTCGTTTTTTTTT‑ATTTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTGCGCACAACTTATCTTCATTCGTg         >  1:1162612/1‑100 (MQ=255)
                                                                                      ggTGAACCAGTCG‑‑TTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGc        <  1:1059759/100‑1 (MQ=255)
                                                                                       gTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGc        <  1:470546/100‑1 (MQ=255)
                                                                                         gAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTGCGCACAACTTATCTTCATTCGTGCtg      <  2:1578927/100‑1 (MQ=255)
                                                                                          aaCCAATCG‑TTTTTTTTGAATTTTATAAGATCTATAAAAAACCGTCCGAACTCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTg         <  1:2154360/96‑1 (MQ=255)
                                                                                            ccAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTgg   <  2:2301343/100‑1 (MQ=255)
                                                                                             cAGTCG‑TTTTTTTTGAATTTTATGAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGa  >  2:1600538/1‑100 (MQ=255)
                                                                                             cAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAGACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGATCACCTTATCTTCATTCGTGTtgtg    >  1:975774/1‑98 (MQ=255)
                                                                                                   |                                                                                              
TCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGA  >  NC_000913/107446‑107639

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