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 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 937,983 G→A *204* (TAG→TAA)  lolA → lipoprotein chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913937,9830GA100.0% 37.1 / NA 13*204* (TAG→TAA) lolAlipoprotein chaperone
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (5/8);  total (5/8)

TTTAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAGAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAGCAACATTTGCTGGCT  >  NC_000913/937852‑938101
                                                                                                                                   |                                                                                                                      
tttAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCAcc                                                                                                                 <  2:1079514/139‑1 (MQ=255)
                                                    aGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTgg                                                             >  1:172406/1‑139 (MQ=255)
                                                     gCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGc                                                            <  2:463282/139‑1 (MQ=255)
                                                                              aaaTTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGataat                                                                             <  1:541126/97‑1 (MQ=255)
                                                                              aaaTTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGataat                                                                             >  2:541126/1‑97 (MQ=255)
                                                                                                        cGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTg                                                                                                  <  1:941600/50‑1 (MQ=255)
                                                                                                        cGTCACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTg                                                                                                  >  2:941600/1‑50 (MQ=255)
                                                                                                           cACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGc                                                                                                        >  1:159483/1‑41 (MQ=255)
                                                                                                           cACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGc                                                                                                        <  2:159483/41‑1 (MQ=255)
                                                                                                           cACGGTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAGCAACATTTgct      <  2:172406/139‑1 (MQ=255)
                                                                                                               gTAGATGATCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAGCAACATTTgctggct  <  2:209910/139‑1 (MQ=255)
                                                                                                                  gatgatCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGcaca                              <  1:130829/108‑1 (MQ=255)
                                                                                                                  gatgatCAACGTAAGTAAAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGcaca                              >  2:130829/1‑108 (MQ=255)
                                                                                                                                   |                                                                                                                      
TTTAGCGCGGTGGAGCAGGACGATCAGCGCAGCAGTTATCAACTGAAATCCCAGCAAAATGGGGCTGTGGATGCAGCGAAATTTACCTTCACCCCGCCGCAAGGCGTCACGGTAGATGATCAACGTAAGTAGAGGCACCTGAGTGAGCAATCTGTCGCTCGATTTTTCGGATAATACTTTTCAACCTCTGGCCGCGCGTATGCGGCCAGAAAATTTAGCACAGTATATCGGCCAGCAACATTTGCTGGCT  >  NC_000913/937852‑938101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A