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
A3 F34 I0 R1 41 39.6 1695432 90.3% 1530975 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,026,927 A→T 100% V30E (GTG→GAG)  mgsA ← methylglyoxal synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,026,9270AT100.0% 120.3 / ‑6.7 42V30E (GTG→GAG) mgsAmethylglyoxal synthase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (21/20);  minor base G (0/1);  total (21/21)
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.

CCAACCTGCTGGTCACCCCCCATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTAAGCACTTATC  >  NC_000913/1026792‑1027064
                                                                                                                                         |                                                                                                                                         
ccAACCTGCTGGTCACCCCCCATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCt                                                                                                                                    <  1:737388/143‑1 (MQ=255)
        ctgGGCACCCCCCATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCa                                                                                                                            <  1:843786/143‑1 (MQ=255)
              aCCCCCCTTGGGGCCCTTCACCATCGCGTTGACGTTCATGCCGGTGGCGCGGGAAATTACGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACCTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCAtttgtt                                                                                                                      <  2:251877/143‑1 (MQ=255)
                  gccATTGGGCCACGCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCa                                                                                                                  <  1:111962/142‑1 (MQ=255)
                  cccATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAGATAAAGTCACCGGAAGCATTGCAATCTC‑TTTTG‑ACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGAATTTGTTTGCa                                                                                                                  >  1:843178/1‑143 (MQ=255)
                  cccATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCa                                                                                                                  >  1:128837/1‑143 (MQ=255)
                  cccATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCa                                                                                                                  <  2:283466/143‑1 (MQ=255)
                  cccATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGGTCCTCCCAGCTCCTCAGCCtttgtttgac                                                                                                                  >  1:178968/1‑141 (MQ=255)
                             aCTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATAAAGTACGTGTTGTTCGAGTAGCGGTTGATGCCGTTCCTCCCCGCTCATCAGCATTTGTTTGAGGTGATCGtgtg                                                                                                       >  1:300537/1‑143 (MQ=255)
                                    aTCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCCTTCCTCCCAGCTCATCAGCATTCGCTTGCCGTGCTCGTGTGccaccca                                                                                                >  2:574940/1‑141 (MQ=255)
                                     tCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCGCAGCTCATCAGCATTTGTTTGGAGTGAGCGTGTGccacaggc                                                                                               >  1:2907/1‑139 (MQ=255)
                                        cctggACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCa                                                                                            <  2:153365/139‑1 (MQ=255)
                                            gACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAatat                                                                                        <  1:587885/143‑1 (MQ=255)
                                                tgcgtGCCGGTCGCGCGTGAAATTGTGGTCGCGGTGG‑‑TGCCTGTTGCATGCAGTGCGTGTTGTTCCAGTAACGGTGGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGttt                                                                                    <  2:38951/139‑1 (MQ=255)
                                                     gCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCAGACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCcgcg                                                                               <  1:720749/143‑1 (MQ=255)
                                                      ccGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTCTGCCACCAGCGCAATATGTTTCCgcgc                                                                              >  2:455373/1‑143 (MQ=255)
                                                               cgGGATATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCCCCGGTAAAGt                                                                     >  2:620878/1‑143 (MQ=255)
                                                               cgGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGt                                                                     >  1:794738/1‑143 (MQ=255)
                                                                          ggtgccGGTAG‑‑GGCCTGTTGCATACAGTACGTGTTGTTCCAGTAGCGGTGGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAGTATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCa                                                          <  2:38991/139‑1 (MQ=255)
                                                                          gTTTCCGGTGG‑‑TGCCGTTTGCATACCGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCGCCCAGCTCATCAGCCTTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCa                                                          <  2:161288/143‑1 (MQ=255)
                                                                          cttACCGGTAG‑‑CGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGGTGATGCCGTGCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCa                                                          <  1:51595/142‑1 (MQ=255)
                                                                           ttACCGGTCG‑‑TGCCTGTTGCCTACCGTACGTGTTGTTCCAGTGAAGGGCGATGCCGAGCCTCACAGCCCATCAGCCTGTGTAGGCAGCGGTGGTCGGCGAACCGTGAAACAAGAATACGCGCAGGTAAAGTGCGAGTCGTCAg                                                         >  2:13508/1‑143 (MQ=255)
                                                                                   aG‑‑TGCGTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGGTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATaa                                                 <  1:385706/143‑1 (MQ=255)
                                                                                       tGCTTGTTGCTTACAGTACGGGTGGGTCCAGGATCGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATg                                               <  2:490011/143‑1 (MQ=255)
                                                                                                     aGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAACGTGCGAGCCGCCAGTCCCATCATGTACATCCGTactga                                 >  2:104986/1‑139 (MQ=255)
                                                                                                     aGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATACTGTCCATCAGTACTTa                                 >  1:410484/1‑143 (MQ=255)
                                                                                                      gTACGTGTTGTTGCAGTAGCGGTGGATGCCGTTCCTCCCGGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTaa                                <  2:353585/143‑1 (MQ=255)
                                                                                                       tACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATGATGTACCTCCGTAGtgatc                               >  1:716115/1‑139 (MQ=255)
                                                                                                           tgttgtTCCAGTAGCGTTTGATGCCGTTCCTCCCAGCTCATCACCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTc                           <  2:713047/143‑1 (MQ=255)
                                                                                                            gttgttCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTcc                          >  1:737235/1‑143 (MQ=255)
                                                                                                             ttgttCCAGTAACGGTTGATGCCGTGCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCt                         <  1:329031/143‑1 (MQ=255)
                                                                                                                 tCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAg                     >  2:18476/1‑143 (MQ=255)
                                                                                                                 tCCAGTAACGGTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGCCGTCAGTTCCATAATGTACATCCGTAGTTACCTTTCCTACAg                     >  2:235859/1‑143 (MQ=255)
                                                                                                                       accGGTTGATTCCGCTCCTCCCTGCTCAGCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCTCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACt               <  2:340997/141‑1 (MQ=255)
                                                                                                                        ccGGTCGACGCCGCTCCTCCCAGCTCATCAGCATCTGTTTGCAGTGATCGTGTGCCCCCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTg              <  1:359792/142‑1 (MQ=255)
                                                                                                                           gTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTGGTTAACTTTCCTACAGATTACTGTaa           >  1:251999/1‑143 (MQ=255)
                                                                                                                           gTTGATGCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTaa           >  2:486849/1‑143 (MQ=255)
                                                                                                                               aggCCGGTCCTCCCAGCCCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTAAGCAc       <  1:817395/141‑1 (MQ=255)
                                                                                                                               aTGCCGTGCCTCCCAGCTCATCAGCACTTGTTTGCAGTGATCGCGTGCCTCCAGCGCAATATGTGTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTAAGCAc       <  2:672967/143‑1 (MQ=255)
                                                                                                                                 gCCGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTAAGCACtt     >  1:296798/1‑143 (MQ=255)
                                                                                                                                  ccGTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCCGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGGAGTTAACTTTCCTCCAGAGTCCTGTAAGCACTTa    >  1:26213/1‑143 (MQ=255)
                                                                                                                                    gTTCCTCCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTGCCTCCAGATTACGGTAAGCACTAATc  >  1:553570/1‑143 (MQ=255)
                                                                                                                                         |                                                                                                                                         
CCAACCTGCTGGTCACCCCCCATTGGGCCACTCAACATCGCGTTGACGTTCATGCCGGTCGCGCGGGAAATTAAGTTACCGGTAG‑‑TGCCTGTTGCATACAGTACGTGTTGTTCCAGTAACGGTTGATGCCGTTCCACCCAGCTCATCAGCATTTGTTTGCAGTGATCGTGTGCCACCAGCGCAATATGTTTCCGCGCAGGTAAAGTGCGAGTCGTCAGTTCCATAATGTACATCCGTAGTTAACTTTCCTACAGATTACTGTAAGCACTTATC  >  NC_000913/1026792‑1027064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A