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
A27 F2 I0 R1 73 6005.1 5484070 98.3% 5390840 135.6

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.98.7% 693.1 / 2.5 152pseudogene (1097/3115 nt)mdtFmultidrug efflux pump RND permease MdtF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base . (63/87);  minor base A (1/1);  total (64/88)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.00e-01
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 153 total aligned reads displayed.

GCCTGAAGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAATTCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCG  >  NZ_CP022686/2408723‑2408996
                                                                                                                                          |                                                                                                                                       
gCCTGAAGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAAtc                                                                                                                                        >  1:581848/1‑139 (MQ=255)
     aaGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTAATCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATccc                                                                                                                                  >  2:143992/1‑140 (MQ=255)
        aCGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCcgac                                                                                                                               <  1:255218/140‑1 (MQ=255)
        aCGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCcgac                                                                                                                               <  1:271247/140‑1 (MQ=255)
          ggTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCcgacga                                                                                                                             >  5:552521/1‑140 (MQ=255)
           gTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGAt                                                                                                                            <  3:256055/140‑1 (MQ=255)
            tttATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCTTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGAtt                                                                                                                           >  4:560982/1‑140 (MQ=255)
            tttATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGAAGAATTTCCGCGCCACAA‑TCATCCCGACGAtt                                                                                                                           >  2:643120/1‑140 (MQ=255)
              tATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTATTCAAAACGCTGGTTGAGGCTATCATCCTCGGCTTCCTGGTCATGTATCTGGTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGAtt                                                                                                                           >  7:150529/1‑138 (MQ=255)
               aTCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGGTGAGGCTATCATCCTCGGCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGcc                                                                                                                        <  4:534273/140‑1 (MQ=255)
                    tACGACACCTCAACGTTTATCAATATTTCTATTGAGGAAGTTTTCAAAACGCTGGTTGAGGATATCATCCTCGTCTTCCTGGTCATGTTTCTGTTTTTGCAGATTTTCCGCGCCACAA‑TCATCCCGACGATAGCCGTa                                                                                                                     <  8:94842/138‑1 (MQ=255)
                    tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCTCCACAA‑TCATCCCGACGATTGCCGTAcc                                                                                                                   >  4:129162/1‑140 (MQ=255)
                    tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATccc                                                                                                                                  >  2:41659/1‑125 (MQ=255)
                    tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATccc                                                                                                                                  <  1:41659/125‑1 (MQ=255)
                    tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTAcc                                                                                                                   <  2:71005/140‑1 (MQ=255)
                    tACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCGGGTCATGTATCTGATTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTAcc                                                                                                                   >  4:660256/1‑140 (MQ=255)
                     aCGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGAATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTAccc                                                                                                                  >  1:61761/1‑139 (MQ=255)
                       gACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCAGACGATTGCCGTAcag                                                                                                                  >  8:308755/1‑136 (MQ=255)
                          accacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCggtggt                                                                                                             <  1:529321/140‑1 (MQ=255)
                          accacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCggtggt                                                                                                             >  3:561639/1‑140 (MQ=255)
                           ccacaccGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGtt                                                                                                            <  1:625415/140‑1 (MQ=255)
                            cacacaGTTTATCAAAATTTCTATTCAGGAAGTATTCAAAACCCTGGTTGAGGCAAACATCCACCTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTACAGCGCCACAA‑TAATCACGACGATAGCCGTACCGGTGCTTa                                                                                                           >  4:690484/1‑140 (MQ=255)
                                 cGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATtctc                                                                                                      >  4:96413/1‑140 (MQ=255)
                                   tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCgg                                                                                                    >  3:224850/1‑140 (MQ=255)
                                   tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCgg                                                                                                    >  6:635163/1‑140 (MQ=255)
                                   tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCgg                                                                                                    >  6:527743/1‑140 (MQ=255)
                                   tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCACGACGATTGCCGTACCGGTGGTTATTATCgg                                                                                                    >  6:281902/1‑140 (MQ=255)
                                   tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCAGCGCCACAA‑TCATCCCGACGAGTGCCGTACCGGTGGTTATTCTAgg                                                                                                    >  5:20181/1‑140 (MQ=255)
                                   tttATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTAAAGCGCCACAA‑TCATCCCGACGATTGCCCTCACGGTGGTTATTCTCgg                                                                                                    >  6:88310/1‑140 (MQ=255)
                                     tataAAAATTTCTATTAATGAAGTTTTCAAAACGATGTTTGAGGCTATCATCCTCGTCTTCCTGGTCATTTATCTTTTTTTGAAGAATTTCCGAGCCACAA‑TCATCCCGACGAATCACGTACCGTAGGTTATTCTCGGGa                                                                                                  >  2:292911/1‑140 (MQ=255)
                                     tATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTACCTGGTCATGTATCTGTTTTTGCAGAATTTCAGCGCCACAA‑TCATCCCGACGCTTGCCGTACCGGTGGTTATTCTCgg                                                                                                    >  8:585962/1‑138 (MQ=255)
                                     tATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCAGCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAAATTCAGCGCCACAA‑TCAGCCCGACGATTCCCGAGACGGTGGTTATTCTCgg                                                                                                    >  7:98214/1‑138 (MQ=255)
                                               tCTATTCAGGAAGTTTTCAAAACGCTGGGTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCg                                                                                          <  7:273165/138‑1 (MQ=255)
                                                          aGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGGCATGTATCTCTTTTTGCAGAATTTTCGCGCAACAA‑TAATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTcggcgg                                                                             <  6:393041/140‑1 (MQ=255)
                                                           gTTTTCAAAACGCTGGTTGAGGATATCATCCTCTTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCTGGACGTTTGCGATCTTGTCGGcggt                                                                            <  5:664951/140‑1 (MQ=255)
                                                           gTTTTCAAAACGCTGGGTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGcggt                                                                            <  2:616004/140‑1 (MQ=255)
                                                             tttCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGCTACGTTTGCGATCTTGTCGGcggtcg                                                                          >  6:30811/1‑140 (MQ=255)
                                                                 acaccGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGttt                                                                      <  1:689626/136‑1 (MQ=255)
                                                                 aaaaCGCTGGTTGAGGATATAATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGACACAA‑TCATCCCGACGATTGCAGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGttt                                                                      <  5:281801/140‑1 (MQ=255)
                                                                  aaaCGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTc                                                                     <  1:123385/140‑1 (MQ=255)
                                                                        tGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGGCGGTTTCACCATc                                                               <  6:359046/140‑1 (MQ=255)
                                                                        tGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATATGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCa                                                                 >  7:307501/1‑138 (MQ=255)
                                                                          gTTGAGGCTATCATCCTCGTCTTCCTTGTAATGTATCTGTTTTTGCATAATTTACGCGCCACAA‑TCATCCCGTCGATTGCCGTACCGGTGGTTATTCTAGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCaa                                                             <  3:323493/140‑1 (MQ=255)
                                                                             gAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCAGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAacac                                                          >  2:518822/1‑140 (MQ=255)
                                                                              aGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACg                                                         <  1:171686/140‑1 (MQ=255)
                                                                               ggCTATCATCCTCGTCTTCCTGTTTATGTATCTGTTTTTTCAGAATTTCCGGGCCACAA‑TCATCCCGACGATTGCCGTACGGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGTCGGTCGGTTTCACCATCAACACGt                                                        <  3:471677/140‑1 (MQ=255)
                                                                                  tATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTaa                                                     <  4:224850/140‑1 (MQ=255)
                                                                                  tATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTaa                                                     <  4:319301/140‑1 (MQ=255)
                                                                                    tcatcGTCGTCTTCCTGGTCATTTATCTGTTTTTGCAGAATTTCCGCGCCA‑AAATCATCCCGACTATTGCCGTACAGGTTGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACt                                                   <  2:369265/140‑1 (MQ=255)
                                                                                    tcatcCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCCCCATCAACACGTTAACt                                                   >  5:70665/1‑140 (MQ=255)
                                                                                    tcatcCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACt                                                   <  3:142972/140‑1 (MQ=255)
                                                                                    tcatcCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACt                                                   <  4:97678/140‑1 (MQ=255)
                                                                                    tcatcCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACt                                                   <  5:305985/140‑1 (MQ=255)
                                                                                    gcatcCTCGGCTTCCTGGTCAAGTATCTGTTTTTCCAGAATTTCCGCGCCACAA‑TCATCCCGACGAGTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACt                                                   <  6:385230/139‑1 (MQ=255)
                                                                                         cTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              >  5:111868/1‑140 (MQ=255)
                                                                                         cTCGTCGTCCTTGGCATGTATCTGTGTTTGAAGATTTTCCGCTCCACAA‑TCATCACGTCGATTGCCGGACCGGTGGTTTTGCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCCTCTACACGTTAACTATg                                                <  8:106495/138‑1 (MQ=255)
                                                                                          tCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACCCGTTAACTATGttg                                             >  2:417569/1‑139 (MQ=255)
                                                                                           cGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGtt                                              >  8:184765/1‑138 (MQ=255)
                                                                                           cGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATACTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTAtttt                                              >  7:441294/1‑138 (MQ=255)
                                                                                            gTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTAATCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCgg                                           >  3:182551/1‑140 (MQ=255)
                                                                                              cTTCCTGGTCATTTATCTGTTTTTGCAGATTTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGGTATTCTCGGGACGTTTGAGAGCTTGTCGTCGGTCGGTTTCACCATCAACACGTTAACTTTGTTCGGGa                                         <  5:651016/140‑1 (MQ=255)
                                                                                              cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCgg                                           <  7:47352/138‑1 (MQ=255)
                                                                                              cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  3:570306/140‑1 (MQ=255)
                                                                                              cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  6:637813/140‑1 (MQ=255)
                                                                                              cTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  6:280926/140‑1 (MQ=255)
                                                                                              cTTCCTGGTCATGTATCTGTTGTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  3:618975/140‑1 (MQ=255)
                                                                                              cTTCATGGTCATGTATCTGTTTTTTCTGAATTTCCGCGCCACAA‑TGATCCCGACGATTGCCGTACCGGTGGTTATTCTAGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGa                                         <  2:549757/140‑1 (MQ=255)
                                                                                              cTTCATGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCTATCTTGTCGGCGGTCGGTTTCACCATCAACCCGTTAACTATGTTCGGGa                                         <  5:88310/140‑1 (MQ=255)
                                                                                               ttCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGAt                                        >  2:250804/1‑140 (MQ=255)
                                                                                                 ccTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATgg                                      >  5:557653/1‑140 (MQ=255)
                                                                                                   tGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCCTCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATgg                                      <  7:642898/138‑1 (MQ=255)
                                                                                                   tGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATgg                                      >  7:192923/1‑138 (MQ=255)
                                                                                                    ggTCATGTATCTGTTTTTGCAGTATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGc                                   <  1:692007/140‑1 (MQ=255)
                                                                                                    ggTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGc                                   <  1:134600/140‑1 (MQ=255)
                                                                                                     gTCATGTATCTGTTTTTGCAGAAATTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGTGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTg                                    <  7:128183/138‑1 (MQ=255)
                                                                                                      tCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTg                                 >  3:498529/1‑140 (MQ=255)
                                                                                                          gTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTTTTCTCGGGACGTTTGCGATCATGTCGGCGGTCGGTTTCACCATCAACACGATAACTATGTTCAGGATGGTTCAGGc                               >  8:529457/1‑138 (MQ=255)
                                                                                                          gTATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGa                             >  2:37703/1‑140 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGTTTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  6:426498/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  1:215391/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  4:585198/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  1:397455/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  3:612727/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGGTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  2:692879/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGGGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGAt                            <  4:455012/140‑1 (MQ=255)
                                                                                                           tATCTGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCAGTACCGGTGGTTATTCTCGGGACGTGTGCGATCTTGTCGGCGGTCGGTTTCCACATCAACACGTTAACTATGTGAGGGATGTTGCTGGCGAt                            >  4:365452/1‑140 (MQ=255)
                                                                                                           tATCTGTTGTTGCAGAAATTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACTTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGTCg                              <  8:346438/138‑1 (MQ=255)
                                                                                                               tGTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCAACAACAACACGTTAACTATGTTAGGGATGGTGCTGGCGATAggg                        >  5:379300/1‑140 (MQ=255)
                                                                                                                gTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       <  6:205105/140‑1 (MQ=255)
                                                                                                                gTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       >  1:563168/1‑140 (MQ=255)
                                                                                                                gTTTTTGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       <  5:415410/140‑1 (MQ=255)
                                                                                                                 tttttGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATtctc                                                                                                      >  7:596196/1‑60 (MQ=255)
                                                                                                                 tttttGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATtctc                                                                                                      <  8:596196/60‑1 (MQ=255)
                                                                                                                  ttttGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGATAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       <  8:192923/138‑1 (MQ=255)
                                                                                                                  ttttGAAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGt                       <  8:413114/138‑1 (MQ=255)
                                                                                                                     tGCAGAATTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACtg                  >  4:495310/1‑140 (MQ=255)
                                                                                                                          aaTTTCCGCGCCACAA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGAGGGTGCTGGCGATAGGGTTACtggtg               <  7:308988/138‑1 (MQ=255)
                                                                                                                                cgcgCCACAA‑TCATCCCGACGTTTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGc       <  3:99713/140‑1 (MQ=255)
                                                                                                                                     cacaA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCg  <  1:465421/140‑1 (MQ=255)
                                                                                                                                     cacaA‑TCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCg  <  4:498529/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                       
GCCTGAAGACGGTTTATCCTTACGACACCACACCGTTTATCAAAATTTCTATTCAGGAAGTTTTCAAAACGCTGGTTGAGGCTATCATCCTCGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGCGCCACAATTCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTAACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCG  >  NZ_CP022686/2408723‑2408996

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