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
A21 F59 I0 R1 60 41.1 1578944 90.5% 1428944 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 461,010 C→A 100% T708N (ACT→AAT)  lon → Lon protease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913461,0100CA100.0% 120.4 / ‑6.7 46T708N (ACT→AAT) lonLon protease
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base A (25/18);  total (28/18)
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.

CATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGA  >  NC_000913/460876‑461148
                                                                                                                                      |                                                                                                                                          
cATCCACGTCCACGTACCGGAAGGTGCGACGCCGCTGTGTCATTCTAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTg                                                                                                                                    <  2:162543/143‑1 (MQ=255)
 aTCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGAGCGGTGAGACCAGTCTGCGTgg                                                                                                                                   >  2:608093/1‑143 (MQ=255)
        tccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGCCAGGTa                                                                                                                            >  2:470192/1‑143 (MQ=255)
         ccgcgtTCCGGGAGGTGCGCTGCCGAAAGCTGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTAc                                                                                                                           <  2:190870/140‑1 (MQ=255)
         ccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTTGTGCCGAAGGAGCAATGACGGGTGAGATCAATCTGCGTGGTCAGGtcc                                                                                                                           >  1:176715/1‑141 (MQ=255)
          cacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACt                                                                                                                          >  1:786588/1‑143 (MQ=255)
                ccGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGGGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGAt                                                                                                                    <  1:555289/143‑1 (MQ=255)
                 cGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATc                                                                                                                   >  1:124971/1‑143 (MQ=255)
                    agggTGCGTCGCCGAACGGTGGTCCGAGTGCGGGTATTGCTGTGTGCAGCGCGCTGGTTTCTTGCCTGACCGGTAGCCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCggt                                                                                                                <  2:272955/141‑1 (MQ=255)
                    aaGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCggt                                                                                                                <  1:716167/143‑1 (MQ=255)
                      ggTGCGAGGCCGAAAGATGGTCCGAGTGCGGGTATTGCTATGTGCACCGCGCTGGTTGCGTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCggtgg                                                                                                              <  2:470722/143‑1 (MQ=255)
                       gTGCGCCGCCGAAAGATGGTCCGGGTGCCGGTAATGCTCTGTACACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACGGGTTACGTTAATCTGCGTGGTCAGGTACTGCCGATCggtggt                                                                                                             <  2:476042/143‑1 (MQ=255)
                       gTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCggtggt                                                                                                             <  2:515450/143‑1 (MQ=255)
                            aCGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGGTTCTTGCCAGACCGGTAACCCGGTTCGTGCCGCGGCGGCACTGCGCGGCGCGTTGACACTGCGAGGTCAGCTACTGCCAAGcggcggatggta                                                                                                        >  2:477719/1‑137 (MQ=255)
                              gCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGATCGTGCAGATTTGGCAACGCACCCTTTGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTGgagag                                                                                                      >  1:215260/1‑143 (MQ=255)
                                cGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGCTAAACCGGTACGTGCCGATGTGGCCATGACCGGTGAGACCAATCCGCGTGGTCAGGTACTGCCGCTCGGCGGCTTgaaagaa                                                                                                    >  2:278026/1‑143 (MQ=255)
                                     gATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAGACt                                                                                               >  1:527921/1‑143 (MQ=255)
                                      aTGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTc                                                                                              >  1:481245/1‑143 (MQ=255)
                                              aGTGTCGGTATGGCTATGGGCCCCGCGGTCGTTTCTCGCCTGCCTGGTAACCCGGTTCGTGCCGATGTGGCACTGCCCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCAATCGGTGGTTTTAAAGAAAAACTCCTGGCAgc                                                                                      <  2:410970/143‑1 (MQ=255)
                                                tGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAgcac                                                                                    >  1:528056/1‑141 (MQ=255)
                                                  ccGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTCACCTGTAACCCGGTTCGGGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCAt                                                                                  >  2:15253/1‑143 (MQ=255)
                                                       aTTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTAGTGCCGACCGGTGGTTCGACAGCAAAACTCCTGGGAGCGCATCgcgg                                                                             >  2:199590/1‑143 (MQ=255)
                                                           cTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAGTGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCggg                                                                         >  1:451647/1‑143 (MQ=255)
                                                              tgtgCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTGCGTGCCGATGTGGCAGTGAGCGGTGAGATCACTCGGCGTGGTCGGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGGtt                                                                      >  1:342040/1‑143 (MQ=255)
                                                                 gCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGAAATaaa                                                                   >  1:738713/1‑143 (MQ=255)
                                                                  cgccGCGCTGGTGTCTCGCGTGACCCGGAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTaaaa                                                                  <  2:374431/141‑1 (MQ=255)
                                                                     cgcgCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAg                                                               >  1:642942/1‑143 (MQ=255)
                                                                      gcgcTGGTTTCTTGCCTGCCCGGTAACCCGGTTCGTGCGGAGGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGGACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGt                                                              <  2:325549/143‑1 (MQ=255)
                                                                               tCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAACACAGTGCTAATTcc                                                     >  1:368999/1‑143 (MQ=255)
                                                                                 ttGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCgg                                                   >  2:370974/1‑142 (MQ=255)
                                                                                    ccTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGCTGAAAACAGTGCTAATTACGTTCg                                                >  1:592794/1‑143 (MQ=255)
                                                                                                 ccGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTCGTCAGGTACTGCCGATCGGTGGTTGGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGAATAAAACAGTACAAATTCCCTTCGAAAATCAACGCGa                                   >  2:511801/1‑143 (MQ=255)
                                                                                                  cGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATACACGCGAt                                  >  1:392080/1‑143 (MQ=255)
                                                                                                    gTTCGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTCCGAAAATAAACGCGATcg                                >  2:193074/1‑142 (MQ=255)
                                                                                                      tCGGGCCGGTGGGGCACTGATCGGTGAGAGCAATCTGCGTGGTCAGGTGCTGCCGATCGGTGGTTTGAATGAAAGTCTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTgg                              <  2:746645/143‑1 (MQ=255)
                                                                                                      gcGTGCCGAGGTAGCAATCGCGCGTGAGATCAATCTGCGTGCTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTgg                              <  2:334089/142‑1 (MQ=255)
                                                                                                       cGTGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGa                             <  1:694593/143‑1 (MQ=255)
                                                                                                         tGCCGATGTGGCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGAGCTGGAag                           >  1:101204/1‑143 (MQ=255)
                                                                                                               tgtgGCGGTGCCCGGTGAGATCAATCTGCGGGGTCAGGGACTGCCGCTCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTc                     <  2:570042/143‑1 (MQ=255)
                                                                                                                 ttgaacagACCGGGTAGATCGATCTGCGTGGTAAAGGACTGCCGGTAGGGAGTGTGAAAGAACGAGTCGTTTCTGCCGATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCt                   <  2:93616/136‑1 (MQ=255)
                                                                                                                 tgGCAATGACCGGTGTGATGAATCTTGGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGAGCATCGCGGCGGGATTAAAACAGGGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCt                   <  2:255532/143‑1 (MQ=255)
                                                                                                                   gCAATGACCGGTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGACAGAATAACTCCTCGCAGCTCATCGCGACGGGATTAAAACAGTGCTAATTCCGTTAGAAAATAAACGCGATCTGGAAGAGATTACTGa                 >  1:130212/1‑143 (MQ=255)
                                                                                                                       ttattggTGAGATTAATCTGCGTGGTCAGGTACGGCCGAACGGTGGCTTGAAAGAAAGACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAAc             <  1:338/138‑1 (MQ=255)
                                                                                                                            ggTGAGATCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGTACGAGAATCCTCACAAAGTAAt        >  2:662240/1‑143 (MQ=255)
                                                                                                                                  aTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAGATAAAAGCGATCTCGAAGAGATTCCTGACAACGTAATTGccca  >  1:327060/1‑141 (MQ=255)
                                                                                                                                  aTCAATCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGa  >  1:766653/1‑143 (MQ=255)
                                                                                                                                      |                                                                                                                                          
CATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGA  >  NC_000913/460876‑461148

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A