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
A3 F76 I0 R1 30 23.0 980404 89.1% 873539 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% 47.4 / NA 17P1100Q (CCG→CAG) rpoBRNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (8/9);  total (8/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAA  >  NC_000913/4184404‑4184673
                                                                                                                                           |                                                                                                                                  
cTGGCGGTTAAACTCCGTATCCAGCCTGGTGAGAAGATGGCAGGTCGTCACGGTAACAAGGCTGTAATTTCTAAGATCTACCCGATCGAAGATATGCCTTACCATGCAAAAGGTACTCCGGTAGACATCGTACTGAACCAGCt                                                                                                                                 <  2:59069/143‑1 (MQ=255)
 tGGCGGTTAAACGCCGTATGTAGCCTCGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTCCTGAACCAGCTg                                                                                                                                >  2:60040/1‑143 (MQ=255)
   gCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTggg                                                                                                                              <  1:424647/143‑1 (MQ=255)
              ccGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtctc                                                                                                                   >  1:136755/1‑143 (MQ=255)
                 tATCCAGCCTGTTGACATGATTGCGTGTCGTCAGGGTAACAAGGGTGTAATTTCTAATATCGACCCGATCGACGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAACTGGGCGTACCGTCTCGTa                                                                                                                <  2:367821/143‑1 (MQ=255)
                                    aTGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAAGCACCGGACTGAACCAGCTGGGCGTACCGTCTCGAATGAACATCGGTCAGGTCCt                                                                                             >  2:262167/1‑143 (MQ=255)
                                        cAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGCACCGTCTCGGATGAGCATCGGTCAGATACTCCaa                                                                                         >  2:160955/1‑143 (MQ=255)
                                         aGGTCGTCACGGTAACGAGGGTGTAATTTCTAAGAGCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                        <  1:194888/143‑1 (MQ=255)
                                                               gtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGac                                                                  >  2:294951/1‑142 (MQ=255)
                                                                tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                 >  1:429674/1‑143 (MQ=255)
                                                                 aaTTTCTAAGATCATCCCGATCGAAGATATGCCTTACGACGAAAACGGTACGCCGGTCGACCTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                <  1:66262/143‑1 (MQ=255)
                                                                 aaTTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAg                                                                <  1:323095/143‑1 (MQ=255)
                                                                             cAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACa                                                    >  2:201954/1‑143 (MQ=255)
                                                                                           atatGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAATGCCATg                                      <  2:133270/143‑1 (MQ=255)
                                                                                                  ttACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCCGGGCATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCCTGCCGAAAc                               >  2:431531/1‑143 (MQ=255)
                                                                                                            aaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTCCCCTCTCAGGGCATCGTCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaaga                     <  1:109495/143‑1 (MQ=255)
                                                                                                                               gcGTACTGAACCAGCTGGGCGCACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGaa  <  1:214415/142‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                  
CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAA  >  NC_000913/4184404‑4184673

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