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
A13 F25 I1 R1 24 37.7 1533230 90.5% 1387573 141.3

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_0009134,184,5430CA89.3% 70.0 / NA 29P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (1/0);  major base A (12/13);  minor base G (0/3);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 2.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184403‑4184681
                                                                                                                                             |                                                                                                                                          
tCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCCGc                                                                                                                                          >  1:745456/1‑143 (MQ=255)
   ggCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTgg                                                                                                                                       <  1:99119/143‑1 (MQ=255)
           aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCATACTGA‑ACCAGATGGGCGTACCg                                                                                                                               >  2:708226/1‑143 (MQ=255)
            aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTCGCCACAGTAGTGA‑CACAGCGGGGCGGACCGt                                                                                                                              >  2:364333/1‑143 (MQ=255)
            aCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGt                                                                                                                              >  1:307590/1‑143 (MQ=255)
             cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTAAGGCGGTCGACATCGTACTGA‑ACCAGCTGTGCGTAcagga                                                                                                                             >  2:656224/1‑139 (MQ=255)
               ccGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGactc                                                                                                                           <  1:442106/143‑1 (MQ=255)
                cGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAGAAAGGCACGCCGGTAGACCTCGTACTGA‑ACCAGCTGGGCGTACCGTCTCg                                                                                                                          >  1:476472/1‑143 (MQ=255)
                  gagccAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTa                                                                                                                        <  1:197376/140‑1 (MQ=255)
                      cAGCCTGGGGGCAAGTTGGCAGGTCGTAACGGTAACAAGGGTGGAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGaa                                                                                                                    <  1:362088/143‑1 (MQ=255)
                             gggagaaGGTGGCAGGTCGTGAGGGGAACAAGGGTGGAATGTCTAAGATCAACCCGATGGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACAGCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATCGGt                                                                                                             <  2:660483/138‑1 (MQ=255)
                                            gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAAcc                                                                                              >  2:688292/1‑143 (MQ=255)
                                            gtcgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAGCCTGGAAAcc                                                                                              >  1:208148/1‑143 (MQ=255)
                                                      tAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTa                                                                                    <  1:346009/143‑1 (MQ=255)
                                                                            aTCCACCTGATCGAAGATATGCCTTCCGGTGGAAGCCGTACGCCGGTAGACATCGTACTGA‑CCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                              <  1:616161/143‑1 (MQ=255)
                                                                            aTCCACCCGATCGAAGATATGCCTTACGATGAAAACGGTCCGCCGGTTGCTTTATGACCGACACAGAATTTTTGT‑TCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                              <  2:339481/143‑1 (MQ=255)
                                                                               ggcccGATCGAAGTTGTGTGTTACGAGGGATACGGGAGGCTGGTAGACATCGTACTTA‑GCCAGCAGGGCGAACCGTCTCGTATGAACATCGGTCAGATCCTAGAAACCCACCTGGGTATGGGTGCGAAAGGTATCGGCGACaa                                                           <  2:328973/141‑1 (MQ=255)
                                                                                 cccGATCGAAGATATGCCTGACGATGAAAACGGTACGCCATTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                         <  1:733153/143‑1 (MQ=255)
                                                                                       cGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGCCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGACCGGTATCGGCGACCAGATCAACg                                                   >  2:461158/1‑143 (MQ=255)
                                                                                            atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTAGCGTCTCGTATGAGCATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATg                                              <  2:265974/143‑1 (MQ=255)
                                                                                             tatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGACCATCGGTCAGATCCTCGAAACCCACCTGGGTCTGGCTGCGCAAGGTATCGGCGACAAGATCAGCGccgcgc                                             >  1:53514/1‑139 (MQ=255)
                                                                                             tacgCCTTGCGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑GCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGc                                             <  1:213877/140‑1 (MQ=255)
                                                                                               tGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTg                                           <  1:119066/143‑1 (MQ=255)
                                                                                                tgcTTTCGATGAAACCGGTACGCCGGTAGACATCGTCCTGA‑CCCGGCTGGGCCTACCGTCTGGTATGAGCATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGa                                          <  2:47308/141‑1 (MQ=255)
                                                                                                            aaaCGGTACGCCCGTAGACATCGTACTGA‑ACCAGCTGGGCTTACCGTCTCGTATGAACATCGGTCAGATCCTCGAATCCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaag                              <  2:255355/143‑1 (MQ=255)
                                                                                                              cccgcaCGCCGGTAGACGCCGTACTGA‑ACCGGCCGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaagaa                            <  1:242301/138‑1 (MQ=255)
                                                                                                                                tCGTACTGA‑ACCAGCTGGGCGTACCGTCTCGTATGAACATGGGTGAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCCCGaa          >  1:110981/1‑143 (MQ=255)
                                                                                                                                        a‑aCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCa  >  1:572032/1‑143 (MQ=255)
                                                                                                                                        a‑aCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATGCATccc  >  1:654522/1‑142 (MQ=255)
                                                                                                                                             |                                                                                                                                          
TCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGA‑ACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  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 < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A