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
A23 F67 I1 R1 23 41.0 1710050 87.8% 1501423 142.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,184,543 C→A 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_0009134,184,5430CA97.4% 99.0 / NA 38P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (19/18);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184411‑4184681
                                                                                                                                    |                                                                                                                                          
ttAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTa                                                                                                                                  >  1:407176/1‑143 (MQ=255)
 tAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCCTAc                                                                                                                                 >  1:115539/1‑143 (MQ=255)
      gCCGTATCCAGCCTGGTGCCAAGATCGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtct                                                                                                                            <  1:568928/143‑1 (MQ=255)
       ccGTATCCAGCCTGGTTATAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTGCTAAGATCAACCCGATCTAAGATATGCCTTACGATCAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                           <  2:754875/143‑1 (MQ=255)
           aTCCAGCCGTGCGACAGGATGGCAGGGTGTCACAGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                       <  2:537791/143‑1 (MQ=255)
                  cTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACAGTCTCGTATGAACATc                                                                                                                >  2:691762/1‑143 (MQ=255)
                    ggTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCGGAACAGCgg                                                                                                              >  2:431528/1‑143 (MQ=255)
                      tGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAAACAGCTGGGCGTACCGTCTCGTATGAACATCGGTc                                                                                                            >  1:561378/1‑143 (MQ=255)
                          aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAAACAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                                        >  2:682329/1‑143 (MQ=255)
                                  aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                                >  1:143762/1‑143 (MQ=255)
                                     tcgtcACTTTAACAAGGGTGTAATTTCGACGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAccc                                                                                             <  2:355922/143‑1 (MQ=255)
                                     tcgtcACGGTAACAAGGGTGTAATTTCTAAGATCACCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAccc                                                                                             <  2:502809/143‑1 (MQ=255)
                                           cGGTAACGAGGGTGGAATGTCGAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                       <  1:788510/143‑1 (MQ=255)
                                                aCAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCgggactg                                                                                  >  2:394360/1‑139 (MQ=255)
                                                 gaaGGGTGTAGTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                                 <  2:309948/142‑1 (MQ=255)
                                                 cAAGGGTGTAATTTCTAAGCTCAACCCGCTCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                                 <  2:367231/143‑1 (MQ=255)
                                                   agtgtgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTCCGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCt                                                                               <  1:758481/140‑1 (MQ=255)
                                                    gggTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAACAACCCGTATGAATATAGATCCTATTCTCTAATCCCACCTGGGTATGGCTg                                                                              >  1:757758/1‑143 (MQ=255)
                                                     gcaatAATTTCTATTATTATCTCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                             <  1:749043/139‑1 (MQ=255)
                                                         tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCATATGAACATCAGTAAGATCCTCGAAACCCACCTGGGTATGACTGCGaaa                                                                         >  1:552309/1‑143 (MQ=255)
                                                          aaTTTCTAAGATCATCCCGATCGTAGATATGCCTTACTATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                        <  1:405611/143‑1 (MQ=255)
                                                          aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGCACCTCGGTCAGATCCTCGAACCCCCCCTGGGTATGGCTGCGTAAg                                                                        >  1:200298/1‑143 (MQ=255)
                                                           aTTTCTAAGATCACCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAgg                                                                       <  1:365519/143‑1 (MQ=255)
                                                            tttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGt                                                                      >  2:625213/1‑143 (MQ=255)
                                                               atAAGATCAACCCGAGCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACGTCGTACTGAACCAGCTGGGCGTACCGTCTCGTACGGCCATCTGGACGATCGTCGAAACCCGCCAGGGTGCAGCTGCGagagcgacc                                                                   >  2:145075/2‑138 (MQ=255)
                                                                         cccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCAGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                         >  2:387719/1‑143 (MQ=255)
                                                                            taTCGAACATATGCCGTCCGATGAAGACGGTACGCCGGTAGACATCGTACTGAACCAGCTGCGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACATGATCa                                                      <  2:705668/142‑1 (MQ=255)
                                                                              ttgAAGATATGCCTTACGTCGAAAACGGTACGCCGGTAGACATCGTACTGATCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGTGTATGGCTGCGAAAGGTATCGGCTACAAGATCAAc                                                    <  2:85052/141‑1 (MQ=255)
                                                                              tCGAAGAGATGGCTTACGATGAAAGCGGTGCGCGGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAGCATCGGTTAGATCCTCGACACGCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                    <  2:318850/143‑1 (MQ=255)
                                                                                    atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACCTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGCCGAGAACGACACCATg                                              >  1:109852/1‑143 (MQ=255)
                                                                                    atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGAAACGGAGACAAGATCAACGCCATg                                              >  1:788781/1‑143 (MQ=255)
                                                                                        gCCTTATGATGGCATCAGGACGCTGGTAGACATCGTACTTAACCAGCTTGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGATACCCACCTGGGTATGGCTGCTAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                          <  2:837812/143‑1 (MQ=255)
                                                                                           ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAAACTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAc                                       >  2:509302/1‑143 (MQ=255)
                                                                                                                     aCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc             <  1:394360/143‑1 (MQ=255)
                                                                                                                      cATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGGCCAGATCAACGCCCTGCTGCAACCGCCGCAAGGATTCGCGTAACTgaacc            >  1:837888/1‑139 (MQ=255)
                                                                                                                      cATCGTACTGAACCAGCTGAGCGTACCGTTTCGTATGAACATCGGTCAGATCCTCTAAACCCACATGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGcgcg            <  1:90342/143‑1 (MQ=255)
                                                                                                                            aCTGAACCAGCTGGGCGTAACGTCTCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCa      <  1:53756/143‑1 (MQ=255)
                                                                                                                                aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGCATCAGCCGCCTGCCGTCGCTACGCTGCTCGAATTCGTcta  >  1:15676/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                          
TTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184411‑4184681

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