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
A11 F20 I0 R1 35 38.1 1546666 86.7% 1340959 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,184,5430CA100.0% 119.0 / NA 42P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (26/16);  total (26/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184403‑4184681
                                                                                                                                            |                                                                                                                                           
acTGGCAGTTAAACGCCGGACCCAGCCAGGTGACAAGCTGGCAGGGCGTCACGGTAACAAAGGTCTAATTTCTAAGCGCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCCTACTGAACCAGc                                                                                                                                           <  1:673455/142‑1 (MQ=255)
 cTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCAGTAGACATCGTACTGAACCAGCt                                                                                                                                          >  1:677123/1‑143 (MQ=255)
    gCGGTTAAAGCCCGTATCCAGCTTGTTGACACTCTGGCAGGTCGTCACGGTAACAAGGGTTTAATTTCTAATATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTggg                                                                                                                                       <  2:591473/143‑1 (MQ=255)
          aaaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAcc                                                                                                                                 >  2:133253/1‑143 (MQ=255)
           aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCg                                                                                                                                >  2:555511/1‑143 (MQ=255)
             cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGATGAAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGAAGGTAGCCATCGTACAGAACCAACTGGGCGGCCCGta                                                                                                                              >  2:80468/1‑142 (MQ=255)
                      cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                     >  1:536048/1‑143 (MQ=255)
                              tGACAAGATGGCAGGTCGTCACGGTAACAAGGGCGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTCGACAACGTACTGAACCAGCTGGGCGTACCGTCGCGTCTGAACATCGCTc                                                                                                             >  1:293713/1‑143 (MQ=255)
                               gACAACATGGCCGGTCGTCACGGTTACAAGCGTGTAATTTATAAGATCAACCCGATAGAACATATGTCTCACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                            <  2:413377/143‑1 (MQ=255)
                                   aGATGTCAGGTCGTCACGGTAACAATGGTGTAATTTCGAAGATCGACCCGATCGAAGATATGCCTTACGATGAAATCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATc                                                                                                        <  2:654715/143‑1 (MQ=255)
                                    gATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGACGTACCGTCTCGTATGAACATCGGTCAGATcc                                                                                                       >  1:634874/1‑143 (MQ=255)
                                          aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCCCATATGAACACCGGTCAGATACTCGaaa                                                                                                 >  1:177427/1‑143 (MQ=255)
                                            gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGCTCAGATCCGCGAAAcc                                                                                               >  2:451695/1‑143 (MQ=255)
                                              cggcACGGGAACGAGGGGGTAATTTCTAAGAACAACCCGATCGAAGATATGCCTTACGATGAAACCGGTACGCCGGTAGCCATCGTACTGAACCAGCTGGGCGCACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCa                                                                                             <  1:30076/140‑1 (MQ=255)
                                                  aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGACAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTg                                                                                         >  1:307878/1‑143 (MQ=255)
                                                     gTAGCAAGGGTGTAATTTCGGAGATCAACCCGATCGAAGGTATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAGCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGt                                                                                      <  2:339722/143‑1 (MQ=255)
                                                                 tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGaaa                                                                         <  1:548136/143‑1 (MQ=255)
                                                                      tCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCGGGGGGTGG‑CTGCGAAAGGTAt                                                                    >  2:85058/1‑143 (MQ=255)
                                                                        tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATGGGGCACATCCTCGAAACCGCCCCGGGTATGG‑CTGCGAAACGTACCg                                                                  >  2:436146/1‑143 (MQ=255)
                                                                         aaGATCAACCCGATCGAAGATATACCTTACAATAAAAACATTACGCTGGTAGACATCGTACTGAACCAACTACGCTGACGGTCTCGTATGGACATCGCTCAGACCCTCGAAACCCACCTGGATATGT‑CTGCGAAAGGTCTCgc                                                                 >  2:506119/1‑142 (MQ=255)
                                                                            aTCAACCCGATCGAAGATATACCCTATGATACTGGGTGTGGGCCGTGAGACATCGGACGGAGCCAGCGGGGCGTACCGGCTCGGATGAACAGCGGGCAGATCATCGAAACACACCTGGGAATGG‑CGGCGAAAGGTAGCGGCGa                                                              >  2:340627/1‑143 (MQ=255)
                                                                                aCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAg                                                          >  1:136056/1‑143 (MQ=255)
                                                                                        gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACAGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAACCTCGAAACACACCTGGGTATGG‑CTGCGAACGATAACGGCGACAAGaacaacca                                                  >  2:189227/1‑141 (MQ=255)
                                                                                                 ccTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGCCAAGATCAACGCCATGCTgca                                         >  1:537994/1‑141 (MQ=255)
                                                                                                     tctattaaaaCGGTACGCCGGTAAACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcag                                     <  1:366440/137‑1 (MQ=255)
                                                                                                         tGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATCCTGAAAcacaagc                                 >  2:522922/1‑138 (MQ=255)
                                                                                                          gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGCAACAgcagca                                >  1:94408/1‑143 (MQ=255)
                                                                                                              gcGGGACGCCGGTAGACATCGTACTGAAGCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaagaa                            <  2:119916/142‑1 (MQ=255)
                                                                                                                ggTGCGCCGGTAGACATCGCACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGt                          <  1:134138/143‑1 (MQ=255)
                                                                                                                  tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                        <  1:629093/143‑1 (MQ=255)
                                                                                                                     gCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCACCGCCATGCTGAAACAGCCGCCAGAAATccaaa                     >  1:529095/1‑139 (MQ=255)
                                                                                                                      ccaggaGAAATTGTACTGAACCAGCTGGGCATACCGTAGCGTATGAACAGCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGaa                    <  1:164393/138‑1 (MQ=255)
                                                                                                                      ccGGTAGACATCGTACTGAACCAGCTGGGCGTCACGTCCCGCATTAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGaa                    <  1:727171/143‑1 (MQ=255)
                                                                                                                       cGGTAGACATCGTACTGAACCAGCTGGGCGGACCGTCTCGTCTGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGaaa                   <  1:555511/143‑1 (MQ=255)
                                                                                                                        gggaGACCTCGTACTGAACCAGCTGGGCGTTCCGGCTCGTATGAACGTCGGTCAGATCCGCGAAACCCACCTTGAGATGG‑CTGCGAAAGGTATCGGCGACCAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAAc                  <  2:107451/140‑1 (MQ=255)
                                                                                                                                  gTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTCCGAAAGGTATCGCCGACAAAATCAACGCCATGCTGAAACAGCAGCAAGAAGCTGCGAAACTGCGCGCAtt        >  2:616876/1‑143 (MQ=255)
                                                                                                                                     cggAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCATATCCTCGAAACCCACCTGGGTGTGGTGTGTGAAACG‑AGCAGAGCAAAATTCGACATGATGGTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCAt     <  1:769222/141‑1 (MQ=255)
                                                                                                                                     cTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCAt     >  1:469381/1‑143 (MQ=255)
                                                                                                                                      tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc    >  1:96839/1‑143 (MQ=255)
                                                                                                                                       gAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGGCGCGAAACAGCGCAAAGTCAtac   >  2:74560/1‑141 (MQ=255)
                                                                                                                                        aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACACGATCAACGCCATGCTGCAACAGCAGCAAGAAGTCGCCAAACTGCACGAATTCATCCa  >  1:361510/1‑143 (MQ=255)
                                                                                                                                        aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCa  >  1:94341/1‑143 (MQ=255)
                                                                                                                                            |                                                                                                                                           
TCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGG‑CTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184403‑4184681

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