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
A9 F2 I0 R1 193 6708.0 8620653 98.5% 8491343 136.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NZ_CP022686 2,408,861 Δ1 bp 100% pseudogene (1097/3115 nt) mdtF → multidrug efflux pump RND permease MdtF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0226862,408,8610T.98.9% 853.5 / ‑0.0 186pseudogene (1097/3115 nt)mdtFmultidrug efflux pump RND permease MdtF
Reads supporting (aligned to +/- strand):  ref base T (0/1);  major base . (75/109);  minor base A (0/1);  total (75/111)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.67e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

Only 100 of 188 total aligned reads displayed.

AAGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAATTCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCG  >  NZ_CP022686/2408728‑2408996
                                                                                                                                     |                                                                                                                                       
aaGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCTCGCCACTA‑TCATccc                                                                                                                                  >  3:159254/1‑140 (MQ=255)
      gTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGAt                                                                                                                            >  2:448593/1‑140 (MQ=255)
       tttATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGAtt                                                                                                                           >  6:231054/1‑140 (MQ=255)
         tATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGTAAGTTTTCTAAACGCTGGGTGAGGCTAGCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGc                                                                                                                         <  7:239057/140‑1 (MQ=255)
             cTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTa                                                                                                                     <  1:738457/140‑1 (MQ=255)
               tACGACACCCCACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTAcc                                                                                                                   >  5:504226/1‑140 (MQ=255)
               tACGACACCACCCCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTAcc                                                                                                                   >  8:539107/1‑140 (MQ=255)
               tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCATGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTAcc                                                                                                                   <  1:463158/140‑1 (MQ=255)
               tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCAGGTTGAGGCTATCATCCTCGACTTCTTGGTCATGTATCTGTTATTGCAGAAATTCCGCGCCACAA‑TCAACCCGACGATTGCCGTAcc                                                                                                                   >  8:288489/1‑140 (MQ=255)
                aCGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCACGACGATTGCCGTACCg                                                                                                                  >  7:309810/1‑140 (MQ=255)
                aCGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTAGCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGCCGATTGCCGTACCg                                                                                                                  >  5:444107/1‑140 (MQ=255)
                 cGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCAGACGATTGCCGTACCgg                                                                                                                 >  6:276510/1‑140 (MQ=255)
                    caccacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCggtgg                                                                                                              <  6:766677/140‑1 (MQ=255)
                     accacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCACCCCGACGATTGCCGTACCggtggt                                                                                                             <  4:596346/140‑1 (MQ=255)
                     accacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTACGCGCCACAA‑TCATCCCGACGATTGCCGTACCggtggt                                                                                                             >  2:843070/1‑140 (MQ=255)
                       cacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTa                                                                                                           <  2:505206/140‑1 (MQ=255)
                       cacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGAAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGttt                                                                                                           >  3:634019/1‑139 (MQ=255)
                       cacaccGTTTATCAAAATTTATATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTa                                                                                                           <  8:471558/140‑1 (MQ=255)
                          accGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTAttg                                                                                                        >  6:485938/1‑139 (MQ=255)
                            cGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATtctc                                                                                                      >  6:629815/1‑140 (MQ=255)
                            cGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGGTTTTGCTGAATTTCCGCGCCACCA‑TCATCCCGACGATTGCCGTACCGGTGGttttgctg                                                                                                      >  4:468774/1‑134 (MQ=255)
                              tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCCTCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCTGATTTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCgg                                                                                                    >  4:136330/1‑140 (MQ=255)
                              tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCGGGTTGAGGCTATCATCCTCGTCTTCATGGTAATGTATCTGTTTTTGAAGAATTTCCGCGCCACAA‑TCATCACGACGATTGCCGTACCGGTGGTTATTCTAgg                                                                                                    >  1:525892/1‑140 (MQ=255)
                              cttATCAAAATTTCTATTCAGGATGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCgg                                                                                                    >  4:224320/2‑140 (MQ=255)
                                   cAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGt                                                                                               <  7:539107/140‑1 (MQ=255)
                                      aaTTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAAt                                                                                                                                         >  8:606325/1‑96 (MQ=255)
                                        tatCTATTCAGGTACTTTTCAAAAAGCTGGTTGAGGCTATACTCCTCGTCTTCCTGGTCATGTATCTGTTTTTTCAGAATTTCCGCGCCACAA‑TCCTGCCTACGATTTCCGTACCGGGGGTTATTCTCGGGACGTTTGCg                                                                                          <  7:871372/138‑1 (MQ=255)
                                                   gAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTcggc                                                                               >  8:804023/1‑140 (MQ=255)
                                                         ttCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTcggcg                                                                              <  5:19486/135‑1 (MQ=255)
                                                            aaaaCGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGttt                                                                      <  1:293308/140‑1 (MQ=255)
                                                                cGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCAcc                                                                  <  2:140819/140‑1 (MQ=255)
                                                                cGCTGGGTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGATTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCAcc                                                                  <  4:193407/140‑1 (MQ=255)
                                                                   tGGGTGAGGCTATCATCATCGTCTTCCTTGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATc                                                               <  4:130423/140‑1 (MQ=255)
                                                                    ggTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCa                                                              <  1:823363/140‑1 (MQ=255)
                                                                     gtggatgCTATCATCCTCGTCGTCCTGGTCATGGATCTGTTTTTGCAGAATTTACGCTCCACAA‑TCATCCCGACGATTGCCGTACCGGGGGTTATTCTCGGGACGTTTGAGATCTTGGCGGCGGTCGGTTTCACCAGCaa                                                             <  8:978629/134‑1 (MQ=255)
                                                                     gtggAGGCTATCATCCTCGTCTTCCTGGTCCTGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCaa                                                             <  8:653300/137‑1 (MQ=255)
                                                                     ggtGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCaa                                                             <  6:930922/138‑1 (MQ=255)
                                                                     gagacagCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCaa                                                             <  7:585978/134‑1 (MQ=255)
                                                                     gTTGAGGCTATCATCCTCGTCTTCCTGGTGTTGTATGTGTTTTTGGTGATTTTCGGCGCCTGAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGAAGTTTGCGATCTTGTCGGGGGTCGGTTTCACCATcta                                                             <  1:151727/140‑3 (MQ=255)
                                                                     gTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCaa                                                             <  3:877364/140‑1 (MQ=255)
                                                                     gTTGAGGCTATCATCCTCGGCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCaa                                                             <  3:835070/140‑1 (MQ=255)
                                                                       tGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAaca                                                           <  5:83792/140‑1 (MQ=255)
                                                                        gAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAacac                                                          <  4:444209/140‑1 (MQ=255)
                                                                        gAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTGTTGCAGAATTGCCGCGCCACCA‑TCCTCCCGACGCATGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGGTTCACCATCAacac                                                          <  3:245921/140‑1 (MQ=255)
                                                                          ggCTATCATCCTCGTCTTCCTGGTCTTGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTGTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGt                                                        >  7:668780/1‑140 (MQ=255)
                                                                          ggCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGt                                                        <  2:249011/140‑1 (MQ=255)
                                                                             tATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTaa                                                     <  2:692468/140‑1 (MQ=255)
                                                                             aatcatcCTCGGCTTCCTGGTCATGTATATGTTATTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTaa                                                     <  8:230600/139‑1 (MQ=255)
                                                                               tcatcCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGACACAA‑TCATCCAGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACt                                                   <  6:1040733/140‑1 (MQ=255)
                                                                                    cTCGTCTTCCTGGTCATTTATCTGTTTTTGCAGAATTTCCGCGCCACTA‑TCATCCAGACGATTGCCGTACCGGTGGTTATTCTCGTGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              <  1:368845/140‑1 (MQ=255)
                                                                                    cTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              <  1:2203/140‑1 (MQ=255)
                                                                                    cTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              >  3:373171/1‑140 (MQ=255)
                                                                                    cTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGCACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              <  3:785768/140‑1 (MQ=255)
                                                                                    cTCGTCTTCCTGGGCATGTATCTGTTTTTGCATAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTAGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              <  2:513817/140‑1 (MQ=255)
                                                                                     tCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCTGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACAATCAACACGTTAACTATTTTc                                             >  1:942650/1‑140 (MQ=255)
                                                                                     tCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGAGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTAAGtta                                             >  1:239041/1‑139 (MQ=255)
                                                                                      cGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGGTATTCTCGGGACGTTTGCGAGCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCg                                            >  5:361924/1‑140 (MQ=255)
                                                                                       gTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGTGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCgg                                           >  1:990130/1‑140 (MQ=255)
                                                                                       gTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCgg                                           >  2:596811/1‑140 (MQ=255)
                                                                                       gTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCgg                                           >  5:1025834/1‑140 (MQ=255)
                                                                                         gttCCTGTTCATGTCTCTGTTTTTGCAGAATTTCGGCGCCAC‑ATTCATCCGGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGGCGGTTTCAACATCAACACGTTAACTATGTTCGGGa                                         <  4:659353/139‑1 (MQ=255)
                                                                                         cTTCCTTGTCATGTATCTGTTTTTTCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  6:390442/140‑1 (MQ=255)
                                                                                         cTTCCTTGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGCTTATTCTCGGGACGGTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  5:747379/140‑1 (MQ=255)
                                                                                         cTTCCTTGTCATGTAGCTGTTTGTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  7:1035/140‑1 (MQ=255)
                                                                                         cTTCCTGGTCATGTATCTGTTTTTTCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  4:799443/140‑1 (MQ=255)
                                                                                         cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  1:771436/140‑1 (MQ=255)
                                                                                         cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  1:901377/140‑1 (MQ=255)
                                                                                         cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  6:101962/140‑1 (MQ=255)
                                                                                         cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGAGCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         >  2:851699/1‑140 (MQ=255)
                                                                                         cTTCCGGGTCATGTATCTGTTTTTGCAGAATTTCCGAGCCACAA‑TAATCACGACGATTGCCGTACCGGTTGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGGCTGTTGAACCATCAACACGTTAACTATGTTCGGGa                                         <  7:503670/140‑1 (MQ=255)
                                                                                         attCCTGGTCATTTATCTGTTTTTGCTGAATTTCCGAGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGCTCGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  7:139663/139‑1 (MQ=255)
                                                                                         attCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCCGGACGTTTGCGATCTTGTCGGCTGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  5:227617/139‑1 (MQ=255)
                                                                                            ccTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCCTCCCGACGATTGCCGTACCGGTGGATATTCTCGGGACGTTAGCGATCTTGTCGCAGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATgg                                      >  2:124743/1‑140 (MQ=255)
                                                                                             cTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTATCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATAAACACGTTAACTATGTTCGGGATGGt                                     >  5:887784/1‑140 (MQ=255)
                                                                                               gggcATGTATCTGTGTTTGCAGAATTGCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGc                                   <  5:905652/137‑1 (MQ=255)
                                                                                               ggTCATTGATCTGTTTTTTCAGAATTTACGCGCAACTA‑TCATCTCGACGATTGCCGTAACGGTGGTTATTCTCGGGACGTTTGCGATCTTTTCGGCGGTCGGTTTCACCATCAACTCGTTAACTATGTTCGGGATGGTGc                                   <  8:1005537/140‑1 (MQ=255)
                                                                                               ggTCATGTATCTTTTTTTGCAGAATTTCCTCGCCACAA‑TCCTCCCGCCGATTGCCGTACCGGTGGTTATTCTCGGGAAGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGc                                   <  5:559270/140‑1 (MQ=255)
                                                                                               ggTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCACCACGTTAACTATGTTCGGGATGGTGc                                   >  2:1054280/1‑140 (MQ=255)
                                                                                               ggTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTgg                                   >  6:792563/1‑139 (MQ=255)
                                                                                               ggTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGc                                   >  8:649962/1‑140 (MQ=255)
                                                                                               ggTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGGTTCACCATCAACACGTTAACTATGTTCGGGATGGTGc                                   <  2:89024/140‑1 (MQ=255)
                                                                                               ggTCATGTATCTGTTTTTGCAGAATTTCCGAGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCTCCATCAACACGTTAACTATGTTCGGGATGGTGc                                   <  8:614765/140‑1 (MQ=255)
                                                                                                gTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCt                                  <  8:38680/140‑1 (MQ=255)
                                                                                                gTCAGGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCt                                  <  8:765511/140‑1 (MQ=255)
                                                                                                 tCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTg                                 >  8:86923/1‑140 (MQ=255)
                                                                                                     gTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGa                             >  4:827174/1‑140 (MQ=255)
                                                                                                      tATGTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGGCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  7:637591/140‑1 (MQ=255)
                                                                                                      tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  4:401880/140‑1 (MQ=255)
                                                                                                           gTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       >  5:991383/1‑140 (MQ=255)
                                                                                                           gTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       >  6:953076/1‑140 (MQ=255)
                                                                                                             ttttGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTa                     <  8:570679/140‑1 (MQ=255)
                                                                                                             ttttGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTa                     <  3:516019/140‑1 (MQ=255)
                                                                                                                  cAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGAGCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGTCGATAGGGTTACtggt                >  7:341641/1‑140 (MQ=255)
                                                                                                                     aaTTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGGCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATTGTGCTGGCGATAGGGTTACTGGTGGa             <  1:594971/140‑1 (MQ=255)
                                                                                                                        ttCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGGGTTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTTCTGGTGGATGa          <  7:853589/140‑1 (MQ=255)
                                                                                                                           cgcgCCTCAA‑TCATCCCGACGATTGCCATACCGGTGGGTATTCTCGGGACGTTTGCGAGCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGc       <  8:903853/140‑1 (MQ=255)
                                                                                                                             cgcCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCa     >  1:707075/1‑140 (MQ=255)
                                                                                                                             cgcCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCa     >  4:898176/1‑140 (MQ=255)
                                                                                                                                cacaA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCg  <  4:727581/140‑1 (MQ=255)
                                                                                                                                cacaA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCg  <  2:377074/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                       
AAGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAATTCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCG  >  NZ_CP022686/2408728‑2408996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A