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 I1 R1 521 238.2 12299412 96.0% 11807435 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATTAATGTGAATATATACAATATTTTTAGCACAACGCTATG  >  NC_000913/1956222‑1956404
                                                                                             |                                                                                         
CGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGC                                                                                           >  SRR4302532.733835/1‑94 (MQ=60)
         AATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTA                                                                                  >  SRR4302532.3151823/1‑94 (MQ=60)
         AATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGCTGCTATTTA                                                                                  <  SRR4302532.4469083/94‑1 (MQ=60)
         AATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGCTGCTATTTA                                                                                  <  SRR4302532.5157645/94‑1 (MQ=60)
             AGTCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTAGAAT                                                                              <  SRR4302532.4180604/94‑1 (MQ=60)
                CACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGCTGCTATTTAGAATATA                                                                           <  SRR4302532.5235957/94‑1 (MQ=60)
                  CAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTAGAATATATA                                                                         <  SRR4302532.4938215/94‑1 (MQ=60)
                         GCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGCTGCTATTTAGAATATATATTTATCA                                                                  <  SRR4302532.2703007/94‑1 (MQ=60)
                                          AAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAAT                                                 <  SRR4302532.3500854/94‑1 (MQ=60)
                                                   ATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGCTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATT                                        >  SRR4302532.1416745/1‑94 (MQ=60)
                                                   ATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGCTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATT                                        >  SRR4302532.1416746/1‑94 (MQ=60)
                                                                 AATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATTAATGTGAATATATA                          <  SRR4302532.4818228/94‑1 (MQ=60)
                                                                             CTAAGGAATAACCCAGTTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATTAATGTGAATATATACAATATTTTTAG              <  SRR4302532.757792/94‑1 (MQ=60)
                                                                                         CCAGCTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATTAATGTGAATATATACAATATTTTTAGCACAACGCTATG  <  SRR4302532.2255638/94‑1 (MQ=60)
                                                                                             |                                                                                         
CGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCATTAATTGCTAAGGAATAACCCAGTTGCTATTTAGAATATATATTTATCAGTTTTAGTAATTTAAATCCCATAATTAATGTGAATATATACAATATTTTTAGCACAACGCTATG  >  NC_000913/1956222‑1956404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑