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
A5 F84 I1 R1 23 34.8 1446234 89.3% 1291486 142.8

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_0009134,184,5430CA94.7% 107.0 / ‑6.5 38P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base A (14/22);  total (15/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATC  >  NC_000913/4184404‑4184679
                                                                                                                                           |                                                                                                                                        
cggggggTTAAACGCCGTATCCAGCCGGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATGTCTAAGATTAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCt                                                                                                                                       <  2:130360/138‑1 (MQ=255)
  ggCGGTTAAACGGCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                     <  1:462787/143‑1 (MQ=255)
  ggCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGCAGCTATGCCTTACGATGAAAACGGTAAGCCGGGAGACATCGAACTGAACCAGATgg                                                                                                                                     >  2:599512/1‑143 (MQ=255)
  ggCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTgg                                                                                                                                     >  1:194678/1‑143 (MQ=255)
   gCGGTTAAACGCCGTATCCAGACTGATGAGAGGATGGCAGGTCGTCACGGTAACAAGGGTGTAAGTTCTAAGATCAACCCGATCGAAGATATGCCTTAAGATGAAAACGGTACGCCGGGAGACCTCGGACTGAACCAGGTggg                                                                                                                                    >  2:437594/1‑143 (MQ=255)
          aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGACCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGCACCGAACCCCATGGGCGGAcag                                                                                                                             >  2:644854/1‑141 (MQ=255)
           gcGCCGGATCCGGCCGGGTGAGCATGTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGt                                                                                                                            <  2:324827/142‑1 (MQ=255)
            cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATGGAAGATATGCCTTACGATGAAAACGGTACGCCGACAGACATCGTACGGAACCAGCTGAGCATACCGtc                                                                                                                           >  2:346537/1‑143 (MQ=255)
                gTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                       <  1:462627/143‑1 (MQ=255)
                              gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                         >  1:380903/1‑143 (MQ=255)
                              gACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCa                                                                                                         >  1:41468/1‑143 (MQ=255)
                                   gATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGACGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATcc                                                                                                    <  1:308297/143‑1 (MQ=255)
                                   gATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGACTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGGACCAGCTGGGCGTACCGGCTCGTATGCACATCGGTCAGGTcc                                                                                                    >  1:143670/1‑143 (MQ=255)
                                    aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCt                                                                                                   <  2:381738/143‑1 (MQ=255)
                                       gCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTGTGAGCATGGGTCAGATCCTCGa                                                                                                >  1:628234/1‑143 (MQ=255)
                                                  cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                     <  1:292208/143‑1 (MQ=255)
                                                      aaCAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCCTACGATGATGATGTTACGCTGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTAt                                                                                 <  1:408635/143‑1 (MQ=255)
                                                        cAAGTGTGTAATTTCTAAGATCACCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                               <  1:663850/143‑1 (MQ=255)
                                                         aaGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGc                                                                              >  1:132740/1‑143 (MQ=255)
                                                          aGGGTGTACTGTCTAAGAGCACCCCGAGCGAAGATATGCCTTACGATGACAACGGTACGCCGGTAGACCTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCt                                                                             <  2:274714/143‑1 (MQ=255)
                                                            ggcgtAATTCCTAAGCTCCACCCGATCGAAGATATCCCTTCCGATGAAAACGGTACGCCGGTAGACACCGTCCTGAACAATCGGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                           <  1:453648/140‑1 (MQ=255)
                                                            ggTGTAATTTCTAAGATCAACCCGATCGAAGATAGGCCGTACGATGAAAACGGTACGCCGGTAGACATCGTACGGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGc                                                                           <  1:547308/143‑1 (MQ=255)
                                                                gaaTTTCTAAGATCAACCCGATCGAAGAGATGACGTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                       <  1:23807/142‑1 (MQ=255)
                                                                 aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                      <  1:593251/143‑1 (MQ=255)
                                                                           aTCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGCCTGCGACAGGTATCGGCGa                                                            >  2:245731/1‑143 (MQ=255)
                                                                                 ccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAt                                                      <  1:628643/143‑1 (MQ=255)
                                                                                    aTCGAAGATATGCCTTACGATGAAAACGGTCCGCCGGTAGACATCGTACTGAACCAGCTGGGAGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCaa                                                   <  1:363573/143‑1 (MQ=255)
                                                                                     tCGAAGATAGGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                  <  1:509625/143‑1 (MQ=255)
                                                                                        aaGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGcc                                               >  1:497273/1‑143 (MQ=255)
                                                                                          gATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCGGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCAt                                             <  2:306401/143‑1 (MQ=255)
                                                                                                      gATGAAAACGGTACGCCGGTAGACATCGTACGGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGAAAAAGTTGTATTAGGTTTCGGCTACAAGATCAACGCCATGCTGAAAcagca                                 <  1:304577/143‑1 (MQ=255)
                                                                                                         gAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAACAACGCCAGGCTGAAACAgcagca                              >  2:365631/1‑143 (MQ=255)
                                                                                                                      cGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGGCAGATCCTCGAAACCCACCGGGGTATGGCTGCGAAAGGTAGCGGCGAGAAGATCAACGCCACGCGGAAACAGCAGCAGGAAGACGCGaaa                 >  1:346971/1‑143 (MQ=255)
                                                                                                                            aCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCGGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc           <  2:132740/143‑1 (MQ=255)
                                                                                                                             cATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGcgcg          <  2:497273/143‑1 (MQ=255)
                                                                                                                               tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGCAACAGCAGCAAGCAGTCGCGAAACTGCGCGaa        >  2:171911/1‑143 (MQ=255)
                                                                                                                                  tACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc     <  2:36652/143‑1 (MQ=255)
                                                                                                                                     tGAACCATCTTGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCTACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATc  <  1:611/143‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                        
CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATC  >  NC_000913/4184404‑4184679

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