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
A17 F104 I0 R1 40 45.6 1767846 90.1% 1592829 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% 140.3 / ‑6.7 50P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base A (22/25);  total (23/27)
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.

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184681
                                                                                                                                           |                                                                                                                                          
cTGGCGGGTAAACGCCGTATCCAGCCAGGTGGTAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCt                                                                                                                                         <  1:830024/143‑1 (MQ=255)
          aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCg                                                                                                                               >  1:212818/1‑143 (MQ=255)
           ccGCCGGATCCAGCCTGGGGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGt                                                                                                                              <  1:192686/142‑1 (MQ=255)
              ctgTATCCAGCCTGGTAACAAGGTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                           <  2:218611/141‑1 (MQ=255)
              cgggaTCCAGCGCGGTGACAGGATGGGAGGTCTTCACGGTAACAGGGGCGTAATGGCTAAGAGGAACCCGATCGAAGATATGCCGTACGGTGAGAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                           <  2:347728/139‑1 (MQ=255)
              ccGTATCCAGCCTGGTGACAAGCTTGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGGACGCCGGTAGACACCGTACAGAACCAGCTGGGCGTAcgatgtc                                                                                                                           <  2:772133/143‑7 (MQ=255)
              ccGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                           >  1:253663/1‑143 (MQ=255)
                 tATCCCGCCTGGTGACATGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                        <  2:474441/143‑1 (MQ=255)
                 tATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                        <  1:383955/143‑1 (MQ=255)
                   tCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATg                                                                                                                      <  1:767383/143‑1 (MQ=255)
                     gagcggggTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    <  2:45430/137‑1 (MQ=255)
                     agtccgggTTACAAGATGGCAGGTCGTCACTGTAACAAGGCTGTAATTTCTAATATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGGACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    <  2:145162/137‑1 (MQ=255)
                            gTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGt                                                                                                             <  2:113549/143‑1 (MQ=255)
                             tGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTc                                                                                                            >  1:460241/1‑143 (MQ=255)
                               aCAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAAGTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAg                                                                                                          <  2:748882/143‑1 (MQ=255)
                                 aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                                        >  1:768831/1‑143 (MQ=255)
                                       gCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGCTCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGGACCAGCTGGGCGAACCGCCTCGTATGCACATCGGTCAGAGCCTCGa                                                                                                  >  2:809913/1‑143 (MQ=255)
                                        cAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaa                                                                                                 <  2:464799/143‑1 (MQ=255)
                                         aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGCTCAGATCCTCGaaa                                                                                                >  2:725222/1‑143 (MQ=255)
                                         aGGTCGTCACGGTAACAAGGGTGGAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                <  1:126751/143‑1 (MQ=255)
                                            tcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAccc                                                                                             >  1:302618/1‑143 (MQ=255)
                                            tcgccACCGTAACAAGGGTGCAATCCGTACGATCAACCCGATCGAAGCTATGCCTTACGATGAAAACGGTACGCCGGTACACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAccc                                                                                             <  1:91641/143‑1 (MQ=255)
                                               tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAACCCCAcc                                                                                          >  1:228811/1‑143 (MQ=255)
                                                  cGGTAACAAGGGTGTAATTTCTAAGAGCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCGGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                       <  2:448902/143‑1 (MQ=255)
                                                      aaCGAGCGTGTAATTTGTAAGACGAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGGAACCCACCTGGGTAt                                                                                   <  2:741682/143‑1 (MQ=255)
                                                       aCAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCATCGAAAACCACCTGGGTATg                                                                                  >  2:350150/1‑143 (MQ=255)
                                                        cAAGGGTGTAGTTTCGAGGGTCAACCCGATCCAAGAGATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                                 <  2:672161/143‑1 (MQ=255)
                                                                tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCgcga                                                                         >  2:517784/1‑140 (MQ=255)
                                                                tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                         >  1:624523/1‑143 (MQ=255)
                                                                tAATTTCTAAGATCAACCCGATCGAAGATATGCATTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGACCCTCGAAACCCACCTGGGCATCGCTGCGaaa                                                                         >  2:55307/1‑143 (MQ=255)
                                                                    ttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAAGGGAACGCCGGTAAACATCGTACTGAAACAGCTGGGCGTACCGTCTCGTATGCACATCGGTCAGATCCTCAACAACCACGTGGGTATGGCTGCGAAAGCTa                                                                     >  1:235370/1‑143 (MQ=255)
                                                                       tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGAGTGATTGCGGAAGGTATCg                                                                  >  2:521815/1‑143 (MQ=255)
                                                                        aaGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAACCACCTGGGTGTGGCTGCGAAAGGGATCgg                                                                 >  2:820593/1‑143 (MQ=255)
                                                                           aTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                              >  1:761633/1‑143 (MQ=255)
                                                                              aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                           <  1:438042/143‑1 (MQ=255)
                                                                                cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCCCGCTTGCACGTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGCAAGGTATCGGCGACAAGa                                                         >  1:326267/1‑143 (MQ=255)
                                                                                 ccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTACCGGCGCCAAGac                                                        >  2:667877/1‑142 (MQ=255)
                                                                                  cGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACTAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATc                                                       <  2:409529/143‑1 (MQ=255)
                                                                                             cggacTTACGCCGAGATCGGTACGCCGGTAGCCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCATAGCCTCGAAACCCACCTGGGTATGGCTGCGAAATGTATCGGCGACAAGATCAACGCCATGCt                                            <  2:694553/139‑1 (MQ=255)
                                                                                                          aaaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                               <  2:401852/143‑1 (MQ=255)
                                                                                                           aaaCGGTACGCCGGTAGACATCGTACTGAACCCGCTCGGCGTACCCTCCCGTATGAACATCGGCCCGATCCTCGCAACCCACCTGGGCATCGCTGCCAACGGCACCGCCCACCACCCCCACGCCCTGCTGCCACagcagcccg                              >  2:465204/1‑140 (MQ=255)
                                                                                                            aaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGGCAAGCTCAACGCCATGCTGAAACAGCAGCaaga                             >  2:473393/1‑143 (MQ=255)
                                                                                                              cGGTACGCCGGTAGACATCGTACTGAACCAGCGTGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaagaag                           <  2:7926/143‑1 (MQ=255)
                                                                                                                  aCGCCGGTAGACTACGACCTGACTGTGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgc                       <  2:212818/143‑1 (MQ=255)
                                                                                                                    gCCGATAGACTGCGGACTGAACCAGCGCGGCGTACCGTCTCGTATGCCCATCGGTCGGGTCCTCGTAACCCACCTGCGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                     <  2:389016/143‑1 (MQ=255)
                                                                                                                                  tACTGAGCCAGGTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCATGGAAAGCCAGCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc       <  2:100168/143‑1 (MQ=255)
                                                                                                                                   aCTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCa      <  2:304563/143‑1 (MQ=255)
                                                                                                                                    cTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGGAACAGCAGCAAGAAGTCGCGACACTGCCCGAATTcct     >  2:828280/1‑141 (MQ=255)
                                                                                                                                     tGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc    >  1:277440/1‑143 (MQ=255)
                                                                                                                                       aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCa  >  2:591468/1‑143 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184404‑4184681

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