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 154 26.6 2069536 90.2% 1866721 108.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 2,579,212 G→C A121A (GCC→GCG)  h16_A2374 ← Metallopeptidase, M23B subfamily

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604792,579,2120GC100.0% 16.5 / NA 6A121A (GCC→GCG) h16_A2374Metallopeptidase, M23B subfamily
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (3/3);  total (3/3)

CGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGGGCCACCGGCATGGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGT  >  AM260479/2579082‑2579318
                                                                                                                                  |                                                                                                          
cGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGgcgc                                                                                                          >  1:614168/1‑133 (MQ=255)
cGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGgcgc                                                                                                          >  2:637099/1‑133 (MQ=255)
                                                gcgcCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCcggc                                                         >  1:927858/1‑134 (MQ=255)
                                                               cggccgGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCgcag                                           >  2:308698/1‑133 (MQ=255)
                                                                                                     tCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGgtt    <  1:637099/134‑1 (MQ=255)
                                                                                                       gATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGgttgt  <  1:308698/134‑1 (MQ=255)
                                                                                                                  ccTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCAc                                                              >  1:71901/1‑63 (MQ=39)
                                                                                                                  ccTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCAc                                                              <  2:71901/63‑1 (MQ=38)
                                                                                                                                  |                                                                                                          
CGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGGGCCACCGGCATGGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGT  >  AM260479/2579082‑2579318

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCTTCATCGAGCCATCGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGGGCCACCGGCATGGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTTCCACGTTGCCACAT  >  AM260479/2579067‑2579333
                                                                                                                                                 |                                                                                                                         
GCTTCATCGAGCCATCGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCC                                                                                                                        >  GWNJ‑0478:712:GW2002102894th:2:2106:19570:62392/1‑149 (MQ=60)
                  acacccacaattcccactccgatccgtagtcctttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGC                                                                                                     <  GWNJ‑0478:712:GW2002102894th:2:2116:3717:48804/42‑1 (MQ=60)
                                                ccgggcacggtGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCG                                                                       >  GWNJ‑0478:712:GW2002102894th:2:2210:12981:2595/12‑150 (MQ=60)
                                                                                                                  GGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtc     >  GWNJ‑0478:712:GW2002102894th:2:1104:2470:96655/1‑93 (MQ=60)
                                                                                                                   GTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTTCCACGTTGCCAC    <  GWNJ‑0478:712:GW2002102894th:2:2109:9045:9054/150‑1 (MQ=60)
                                                                                                                     CGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTTCCACGTTGCCACAT  <  GWNJ‑0478:712:GW2002102894th:2:1205:12314:70581/150‑1 (MQ=60)
                                                                                                                                                 |                                                                                                                         
GCTTCATCGAGCCATCGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGGGCCACCGGCATGGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTTCCACGTTGCCACAT  >  AM260479/2579067‑2579333

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑