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
A10 F169 I0 R1 76 156.9 7610945 95.9% 7298896 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.90.5% 389.0 / 34.6 105intergenic (+71/‑160)lpxC/secMUDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation
Reads supporting (aligned to +/- strand):  ref base T (7/2);  new base . (50/45);  total (57/48)
Fisher's exact test for biased strand distribution p-value = 1.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.73e-01

Only 100 of 119 total aligned reads displayed.

TCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAC  >  NC_000913/107446‑107640
                                                                                                   |                                                                                               
tCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGt                                                                                                 >  1:53796/1‑100 (MQ=255)
 cAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTCTACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtt                                                                                                >  2:2682906/1‑100 (MQ=255)
   aaGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtttt                                                                                              >  2:2368989/1‑100 (MQ=255)
    aGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttt                                                                                             >  1:1192125/1‑100 (MQ=255)
      cgcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttt                                                                                           <  2:2307437/100‑1 (MQ=255)
      cgcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTACAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttt                                                                                           <  1:2660053/100‑1 (MQ=255)
       gcCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGtttttttg                                                                                          <  1:1789769/100‑2 (MQ=255)
        ccTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttt                                                                                         <  1:3030947/100‑1 (MQ=255)
         cTTCCGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttga                                                                                        >  1:226009/1‑98 (MQ=255)
         cTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttga                                                                                        >  2:2203166/1‑98 (MQ=255)
           tCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttgaat                                                                                      >  2:265639/1‑96 (MQ=255)
            cAGCTGTACTGGCATAACGACATTTATACGGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGttttttttgattt                                                                                     >  1:412623/1‑95 (MQ=255)
               cTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATTTGGCACTCTCTCCTGCGAGGTGAACCAGTCG‑TTTTTTTTGAATTTta                                                                                 <  1:2492209/100‑1 (MQ=255)
               cTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTta                                                                                 <  1:3623773/100‑1 (MQ=255)
               cTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTta                                                                                 <  2:69281/100‑1 (MQ=255)
                 gTACTGTCATATCGCCATTTTTACTCTCGCATAAAATTGGCCTCGCAAATCTTTCACTTTCTCCGCCCAGGTGAACCAGTCGTTTTTTTTT‑AATTTtat                                                                                <  1:1438467/99‑1 (MQ=255)
                  tACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATaa                                                                              >  1:1279535/1‑100 (MQ=255)
                    cTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAaga                                                                            <  1:1839802/100‑1 (MQ=255)
                     tGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAagag                                                                           <  2:2753146/100‑1 (MQ=255)
                      ggCCTAACGACGTTTATACTGACCTATAAAATACGACTGGCAAATCTGTAACTATCGTCGGCGAGGTAAACCACTCG‑TTTTTATGGAATTTTATgaga                                                                            >  1:933613/1‑98 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAagag                                                                           >  1:1097734/1‑99 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                          >  1:477498/1‑100 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                          >  2:421914/1‑100 (MQ=255)
                      ggCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGc                                                                          >  2:2479603/1‑100 (MQ=255)
                       gCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACAAGTCG‑TTTTTTTTGAATTTTATAagagat                                                                         >  1:3359975/1‑98 (MQ=255)
                        cATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCta                                                                        >  2:180487/1‑100 (MQ=255)
                        cATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCta                                                                        >  2:3059074/1‑100 (MQ=255)
                           aaCGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATaa                                                                     >  1:683019/1‑100 (MQ=255)
                                cATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAAc                                                                <  1:984142/100‑1 (MQ=255)
                                 aTTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTATTTGAATTTTATAAGAGCTATAAAAAAc                                                                >  1:2288972/1‑99 (MQ=255)
                                   ttATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑ATTTTTTTGAATTTTATAAAAGCTATAAAAAACGGt                                                             >  2:699858/1‑100 (MQ=255)
                                    tataCTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTg                                                            <  2:2651682/100‑1 (MQ=255)
                                     ataCTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGc                                                           <  2:1462465/100‑1 (MQ=255)
                                     ataCTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGc                                                           <  2:3248822/100‑1 (MQ=255)
                                        cTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGACTTTTATAAGAGCTATCAAAAACGGTGCGaa                                                        >  1:3260520/1‑100 (MQ=255)
                                        cTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGaa                                                        <  1:3025024/100‑1 (MQ=255)
                                        cTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGaa                                                        >  2:1894913/1‑100 (MQ=255)
                                          gTCGTATAAAATTCGACTGTCAAATCTGTCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACg                                                      <  1:1719161/100‑1 (MQ=255)
                                          gTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACg                                                      >  2:2984823/1‑100 (MQ=255)
                                             gTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGATTTTTATAAGAGCTATAAAACACGGCGCAAACGCt                                                    >  1:1446761/1‑99 (MQ=255)
                                              tataAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACACTg                                                   >  1:573568/1‑99 (MQ=255)
                                                taAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGttt                                                >  2:3646264/1‑100 (MQ=255)
                                                 aaaaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGtttt                                               >  2:2488952/1‑100 (MQ=255)
                                                  aaaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                              <  2:3003695/100‑1 (MQ=255)
                                                  aaaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTc                                              >  2:3498697/1‑100 (MQ=255)
                                                   aaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCt                                             <  2:2423060/100‑1 (MQ=255)
                                                   aaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCt                                             <  2:1344129/100‑1 (MQ=255)
                                                   aaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAAAGAAATAAAAAACGGTGCGAGCGCTGTTTTCt                                             <  1:269999/100‑1 (MQ=255)
                                                     ttCGACTGGCAAATCTGGCACTCTCTCCTGCCATGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTa                                           <  1:1468547/100‑1 (MQ=255)
                                                      tCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTaa                                          <  2:2897650/100‑1 (MQ=255)
                                                       cGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                         <  2:2880258/100‑1 (MQ=255)
                                                       cGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                         <  1:2808631/100‑1 (MQ=255)
                                                        gACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                         <  1:3368987/99‑1 (MQ=255)
                                                          cgcgCAAATCTGGAACTCTCTCCGAACAGGTTAACCAGTAG‑TGTTTTTTGCATTTTATAAGAGCTAGAAAAAACGGTGCGAACGCTGTTTTCTTa                                           <  1:3423291/92‑1 (MQ=255)
                                                          cTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                      >  2:2748491/1‑100 (MQ=255)
                                                           tGGCAAGTCTGGCACTCTCTCCGGCCAGGCGAACCATTC‑ATTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGc                                        <  1:2663296/97‑1 (MQ=255)
                                                           tGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACt                                     >  2:3355324/1‑100 (MQ=255)
                                                           tGGCAAATCTGGCACTCTCTCCGGCCAGCTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCAc                                      <  1:2287159/99‑1 (MQ=255)
                                                            ggCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTT‑TTTTTTTTAAGAGCTATAAAAAACGGTGCGATTTCTGTTTTCTTAAGTACtt                                    >  1:2585077/1‑100 (MQ=255)
                                                            ggCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTT‑TATTTTATAATTGCTCTAACAAACTGTGTGTACGCTGTTTTCTTAAGCACtt                                    >  1:1497664/1‑100 (MQ=255)
                                                            ggCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  2:1271153/1‑100 (MQ=255)
                                                            ggCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtt                                    >  2:1783889/1‑100 (MQ=255)
                                                            ggCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCCGTTTTCTTAAGCACtt                                    >  2:1330328/1‑100 (MQ=255)
                                                             gCAAATCTGGCACTCTCTCGGGCCAAGAAAACCAGTCG‑TTTTTTTTGAATTTTATAAAAAAAAAAAAAAACGGTGCGAACGCTGTTTTCTTAAg                                         <  1:3739940/94‑1 (MQ=255)
                                                             gCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtat                                   >  1:2296219/1‑98 (MQ=255)
                                                              cAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACtttt                                  >  2:2049498/1‑100 (MQ=255)
                                                               aaaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTc                                 <  2:1741815/100‑1 (MQ=255)
                                                                 aTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGCGCTATAACAGACGGTGCGACCGCTGTTTTCTTAAGCACTTTTCCg                               >  1:1437556/1‑100 (MQ=255)
                                                                 aTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAGCGCTGTTTTCTTAAGCACTTTTACg                               >  1:3669806/1‑100 (MQ=255)
                                                                 aTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAAAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCg                               >  2:210911/1‑100 (MQ=255)
                                                                  tCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCg                               <  1:2488073/100‑1 (MQ=255)
                                                                  tCTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGc                              <  1:531827/100‑1 (MQ=255)
                                                                   cTGGCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGca                             >  2:2115927/1‑100 (MQ=255)
                                                                     ggCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcaca                           <  2:1133217/100‑1 (MQ=255)
                                                                     ggCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGcaca                           >  2:1104327/1‑100 (MQ=255)
                                                                      gCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACaa                          >  2:3590239/1‑100 (MQ=255)
                                                                      gCACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACaa                          >  2:3631379/1‑100 (MQ=255)
                                                                       cACTCTCTCCGGCCAGTTGAACCAGTCG‑TTCTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCg                               <  2:2671278/94‑1 (MQ=255)
                                                                       cACTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAAc                         <  2:3693310/100‑1 (MQ=255)
                                                                        aCTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACt                        <  1:1650417/100‑1 (MQ=255)
                                                                        aCTCTCTCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTACGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACt                        >  1:3075712/1‑100 (MQ=255)
                                                                         ctctctCCGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACtt                       >  2:3614740/1‑100 (MQ=255)
                                                                             ctcCGGCCAGGTGAACCAGTCGTTTTTTTTT‑TTTTTTTTAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCt                   >  1:1562260/1‑100 (MQ=255)
                                                                              nccGGCCAGGTGAACCAGTCGTTTTTTTTT‑TTTTTTTTTTTTTTTTTTAAAAACGATGAGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCtt                  >  1:3136660/2‑100 (MQ=255)
                                                                               ccGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCtt                  <  1:1249284/99‑1 (MQ=255)
                                                                               ccGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTc                 <  2:383864/100‑1 (MQ=255)
                                                                                cGGCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCa                >  1:197073/1‑100 (MQ=255)
                                                                                  gCCAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGCACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCAtt              >  2:1366663/1‑100 (MQ=255)
                                                                                   ccAGGTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTc             <  1:3539727/100‑1 (MQ=255)
                                                                                       gTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGc         >  2:164492/1‑100 (MQ=255)
                                                                                       gTGAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGc         <  1:156525/100‑1 (MQ=255)
                                                                                         gAACCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtg       >  2:2160026/1‑100 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTTCtgtg     >  1:2131829/1‑100 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtgtg     <  1:732812/100‑1 (MQ=255)
                                                                                           aCCAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCtgtg     <  2:2008573/100‑1 (MQ=255)
                                                                                            ccAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTgg    >  2:2974154/1‑100 (MQ=255)
                                                                                            ccAGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTgg    >  2:3783810/1‑100 (MQ=255)
                                                                                             cAGTCGTTTTTTTTT‑TTTTTTTTAAAAGCAATAAAAAACAGTGCGAACTCTCTTTTCTTAAGCACTTTTCCGCACCACTTATCTTCATTCGTGCtttttt   >  1:384343/1‑95 (MQ=255)
                                                                                             cAGTCGTTTTTTTTT‑TTTTTTTTAAAAACTAAAAAAAACGATGCGAATTCTGTTTTATTAAGCACTTTTCCGCACAACTTATCTTCATTccttcttttt    >  1:424065/1‑90 (MQ=255)
                                                                                              aGTCG‑TTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAc  <  2:2621776/100‑1 (MQ=255)
                                                                                                   |                                                                                               
TCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGAC  >  NC_000913/107446‑107640

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