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
A19 F50 I0 R1 80 46.5 1794022 91.0% 1632560 142.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,114,431 G→A 100% N14N (AAC→AAT)  fpr ← flavodoxin/ferredoxin‑NADP(+) reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,114,4310GA100.0% 116.0 / ‑6.7 43N14N (AAC→AAT) fprflavodoxin/ferredoxin‑NADP(+) reductase
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (16/26);  total (17/26)
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.

GATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAGTTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAATCGATCAAATCAATC  >  NC_000913/4114292‑4114570
                                                                                                                                           |                                                                                                                                           
gATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTc                                                                                                                                          >  1:741983/1‑143 (MQ=255)
    aTCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCa                                                                                                                                      <  2:676473/143‑1 (MQ=255)
        ggCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTGCAATTCTGCACttt                                                                                                                                  >  1:773030/1‑143 (MQ=255)
             gTTTACATAGGAGTAGGCGCGCTGGACGCGTCCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCGAACTCTGCACTGTAGTGa                                                                                                                             >  2:97325/1‑143 (MQ=255)
                tACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTACATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGCACGGTGAGACTAAACAGGGCGTCGGTGCCGTTCTGCACATGAGTGAcgt                                                                                                                          >  1:885269/1‑141 (MQ=255)
                          tAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTAc                                                                                                                >  1:711372/1‑143 (MQ=255)
                              cgcggTGGAGGCGTTCGCCGTCGCGTTTAAGGCCAAGCTTGGGAAATTGCCCGGCGGGAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACGGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCaa                                                                                                            <  2:330933/143‑1 (MQ=255)
                                 gcTCGAAGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAAGTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGACCGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCa                                                                                                         <  2:887774/143‑1 (MQ=255)
                                      actcgTTCGCTGTCGAGTTCAAGGCCAAGGTTTGGAATTTGCCCGGCGGTAAACGTAAGCCCGGGGGCGTGAACGGTGAGACTAAATATGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCAt                                                                                                    <  2:250550/140‑1 (MQ=255)
                                      aCGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCAt                                                                                                    >  1:439350/1‑143 (MQ=255)
                                          gtgcGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGATCGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGttt                                                                                                <  2:69600/140‑1 (MQ=255)
                                            tCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGttttt                                                                                              >  1:477973/1‑143 (MQ=255)
                                                 gTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCTTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCt                                                                                         <  1:561983/143‑1 (MQ=255)
                                                 gTCGATTACATGGCCAAGCTCGGTAAATTGCTTGTTGTTAAACGGAAGCACGGGGGCGTGAACGGTGAGACGAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCt                                                                                         <  1:282956/143‑1 (MQ=255)
                                                 gTCGAGTTCAAGCCCAAGCTTGCGAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCt                                                                                         <  1:625580/143‑1 (MQ=255)
                                                    gATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGtt                                                                                      >  1:569092/1‑143 (MQ=255)
                                                     tcatCAAGTCTAATCTTGGGCAATGGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTACACCGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCCATCAGCCATGTTTTTCTCCTGttt                                                                                     <  1:645373/140‑1 (MQ=255)
                                                     aTTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTGTCGTGACTTTGCCTGTTACGCGCTGGGCCATGTTTTTCTCGTGttt                                                                                     >  2:677506/1‑143 (MQ=255)
                                                        tCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACCGGGAGTCGGTCCAATTCTGCTCTTTAGAGACTTTGCCTGTTACCGAATCAGCCATGTTTTTCTCCTTTTttga                                                                                  >  2:42371/1‑143 (MQ=255)
                                                         cAAGGGCTAGCTCGGTAAATTCCCCGGCGGTACACGGAAGCACGTGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTttgat                                                                                 <  1:56333/143‑1 (MQ=255)
                                                            ggCCGAGCTTGGTAAATTGCCCTGCGGGAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTttgattga                                                                              <  2:674031/143‑1 (MQ=255)
                                                            ggCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTttgattga                                                                              <  1:821743/143‑1 (MQ=255)
                                                              ccAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACt                                                                            >  2:295412/1‑143 (MQ=255)
                                                                  gcctGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAACCAGCCATGTTTGTCTCCTGTTTTGATTGACTTGcc                                                                        <  2:783528/140‑1 (MQ=255)
                                                                    gtGGTAGATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCtt                                                                      <  2:882414/142‑1 (MQ=255)
                                                                        tagacggCCCGGCGGGAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCt                                                                  <  1:225814/137‑1 (MQ=255)
                                                                                  ggcggTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCg                                                        <  1:111084/143‑1 (MQ=255)
                                                                                    cggTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTCTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGaa                                                      <  1:802264/143‑1 (MQ=255)
                                                                                             gAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAAGTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTCCCTTATCTTCGTTTTACGAACAAAAAAAt                                             >  1:613512/1‑143 (MQ=255)
                                                                                             gAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGCCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAAt                                             >  2:138185/1‑143 (MQ=255)
                                                                                               aGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTc                                           <  1:526678/143‑1 (MQ=255)
                                                                                                      gggCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTccc                                    <  1:310178/143‑1 (MQ=255)
                                                                                                          gTGAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATAAGCAATGTTTTTCTCCTGTTTTGATTGTCTTGCTTTGTCTTCGTTCTCCGAACAAAAAAATTCCAGTCCTGAAg                                >  2:244165/1‑143 (MQ=255)
                                                                                                            gAACGGTGAGACTAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGa                              <  1:500573/143‑1 (MQ=255)
                                                                                                             aaCGGTGACACTCAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTGTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGAc                             <  1:42371/143‑1 (MQ=255)
                                                                                                                   gagaCTACGCAGGGCGTCGGTCCAATTCTGCACTGTCGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCGTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAg                       <  1:205680/143‑1 (MQ=255)
                                                                                                                        tAAACAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCGATGAGCCATGTTTTTCGCCTGTTTTGATTGACTTGCCTTATCGTCGTTCTCCGAACAAAAAGATTCAAGTGCCGAAGGACTGGAAgggtga                  >  2:534258/1‑139 (MQ=255)
                                                                                                                          aaCAGGGCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAAt                >  2:863924/1‑143 (MQ=255)
                                                                                                                               ggCGTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTCTCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGCAGGACTGGAAGGGCCAATCGatc           >  2:507503/1‑143 (MQ=255)
                                                                                                                                  gTCGGTCCAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAATCGatcaaa        <  1:344439/143‑1 (MQ=255)
                                                                                                                                  gTCGGCCCAATTCTGCACGCTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAATCGatcaaa        <  1:138185/143‑1 (MQ=255)
                                                                                                                                   tCGGGCCAATTCTGCACTTTAGTGACTTTGCAGGTTACCCAATCAGCCATGATTATATCTTGTTATGATTGACTTGCCTTATCTTCGTAAAAAAAAAAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAATCGatcaaat       <  2:439350/143‑1 (MQ=255)
                                                                                                                                        ccAATTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAATCGATCAaatcaatc  <  1:7571/143‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                           
GATTATCGGGCGAGTTTACATAGGAGTAGGCGCGCTGGACGCGTTCGCCGTCGATTTCAAGGCCAAGCTTGGTAAATTGCCCGGCGGTAAACGGAAGCACGGGGGCGTGAACGGTGAGACTAAACAGGGCGTCGGTCCAGTTCTGCACTTTAGTGACTTTGCCTGTTACCCAATCAGCCATGTTTTTCTCCTGTTTTGATTGACTTGCCTTATCTTCGTTCTCCGAACAAAAAAATTCCAGTCCCGAAGGACTGGAAGGCTCAATCGATCAAATCAATC  >  NC_000913/4114292‑4114570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A