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
A1 F112 I0 R1 62 38.0 1654010 89.9% 1486954 142.7

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% 125.3 / ‑6.7 41P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (23/17);  total (23/18)
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.

GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAA  >  NC_000913/4184406‑4184673
                                                                                                                                          |                                                                                                                                  
ggCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                               <  1:219079/143‑1 (MQ=255)
   ggTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCg                                                                                                                            >  2:610468/1‑143 (MQ=255)
   ggTTAAACGCCGTATCCAGCCTGGAGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCg                                                                                                                            >  2:200199/1‑143 (MQ=255)
     ttAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTa                                                                                                                          >  1:401489/1‑143 (MQ=255)
      tAAGCGCCGTATCCAGCCCGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAGCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAc                                                                                                                         <  2:524117/143‑1 (MQ=255)
      tAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTACCTACGGTGGTCAATT‑TAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACCGAACCAGCTGGGCGTAc                                                                                                                         <  1:378222/143‑1 (MQ=255)
        aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCg                                                                                                                       >  1:622446/1‑143 (MQ=255)
          cGCCGTACCCAGCCCGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GCAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtc                                                                                                                     <  1:70393/143‑1 (MQ=255)
                   cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                            <  1:578888/143‑1 (MQ=255)
                        tGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCg                                                                                                       <  1:193790/143‑1 (MQ=255)
                           tGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTc                                                                                                    <  1:38628/143‑1 (MQ=255)
                                    ggCAGGTGGTCACGGTAACAAGGGT‑GTAATTTCTAAGCTCAAGCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACAGCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCg                                                                                           <  2:78013/143‑1 (MQ=255)
                                       aGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCAGTCAGATCCTCGaaa                                                                                        >  2:510680/1‑143 (MQ=255)
                                             tcACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGCCAGATCCTCGAAACCCAcc                                                                                  >  1:417726/1‑143 (MQ=255)
                                                       aaGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGc                                                                        >  2:424786/1‑143 (MQ=255)
                                                       aaGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGAATgcc                                                                        >  2:45684/1‑141 (MQ=255)
                                                          ggT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCGGGTATGGCTGc                                                                     >  2:294637/1‑143 (MQ=255)
                                                            t‑gtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGa                                                                   <  1:753389/143‑1 (MQ=255)
                                                               tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTGTGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                 >  1:214466/1‑143 (MQ=255)
                                                                aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                <  2:378004/143‑1 (MQ=255)
                                                                 aTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGATAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTTTGAGCATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCggaggg                                                               >  1:466112/1‑138 (MQ=255)
                                                                    tCTAAGATTAACCCGATCGAAGATATGCCTGACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTAt                                                            <  1:223474/143‑1 (MQ=255)
                                                                            ccaCCCCACCGAAGATATGCCTTACGATGAAAACGGTACCCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACa                                                    <  2:51972/141‑1 (MQ=255)
                                                                               cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCCGATCCTCGAAACCCACCTGGGAATGGCTGCGGAAGGTATCGGCGACaaca                                                 >  2:276146/1‑141 (MQ=255)
                                                                               cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGCACGGCTGCGAAAGTTATAGGCGACAAGa                                                 >  1:798703/1‑143 (MQ=255)
                                                                                   aTCGAAGATATGCCTTACGATGAAAACGGTACGCAAGTAGACTTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGGATTTCGGTTAGAGCCTCGAAACCCACCTGGGGATGTCTGCGCAAGGTTTAGGCGGCaaaactag                                             >  2:15326/1‑137 (MQ=255)
                                                                                                cctACGATGAAAACGGTGCGCCGGTAGACATCGCACGGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAGCCTCGCAACCCACCTGTGTATGTCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                <  2:673091/141‑1 (MQ=255)
                                                                                                cTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                >  1:801307/1‑143 (MQ=255)
                                                                                                cTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAGCAGCGCCATGCGGaaa                                >  2:260682/1‑143 (MQ=255)
                                                                                                 ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTggagc                               >  1:654709/1‑139 (MQ=255)
                                                                                                 ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAGCGGTCAGGTCCTCGAAACCCAGATGGGTATGGACCCGAAAGGTATCGGCGGCAAGGTCAACGCCATGCTGAAAc                               >  1:596876/1‑143 (MQ=255)
                                                                                                        gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAgcagca                        <  1:787470/143‑1 (MQ=255)
                                                                                                         gaaaCGGTACGCCGGTAGACATCGTACGGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                       <  1:5011/142‑1 (MQ=255)
                                                                                                                tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                <  2:401489/143‑1 (MQ=255)
                                                                                                                tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACACACCTGAGTATGGCTGCGAAAGGTATCGGCGACAGGACAAACGCCATGCGGAAGCAGCCGCGAGCAGAcg                >  2:22621/1‑143 (MQ=255)
                                                                                                                       gTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCCTGATCACACAGCAGCAAGAAGTCGCCAAACt         >  2:564871/1‑143 (MQ=255)
                                                                                                                        tAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGGAACTg        >  1:454519/1‑143 (MQ=255)
                                                                                                                         aGACATCGTACTGAACCAGCTGGGCGTACCGTCGCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgc       <  1:406115/143‑1 (MQ=255)
                                                                                                                          tgcATCGTGCTGAAGCAGCTGGGCGTACCGCCTCGTATGAACAGCGGTAAGATGCTCGGAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcg      <  2:824871/141‑1 (MQ=255)
                                                                                                                             aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCCTGCTGAACCAGCAGCAAGAAGTCGCGACACTGCGCGa   >  1:128986/1‑143 (MQ=255)
                                                                                                                              tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCAACCTGGGTATGGCTGCGAAAGGTATGGGCGACAAGAGCAACGCCATGCAGAAACAGAAGCAAGAAGACGAGCAACTGCGCGag  >  1:332354/1‑142 (MQ=255)
                                                                                                                                          |                                                                                                                                  
GGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGT‑GTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAA  >  NC_000913/4184406‑4184673

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