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 152 24.9 2083062 91.6% 1908084 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 3,515,018 C→G noncoding (32/75 nt) tRNA‑Pro (CGG) → tRNA‑Pro

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604793,515,0180CG100.0% 42.1 / NA 12noncoding (32/75 nt)tRNA‑Pro (CGG)tRNA‑Pro
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (7/5);  total (7/5)

CTCTTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACCTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGC  >  AM260479/3514909‑3515136
                                                                                                             |                                                                                                                      
ctctTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGtt                                                                                                <  1:911702/134‑1 (MQ=255)
ctctTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGtt                                                                                                >  2:456881/1‑134 (MQ=255)
             cAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCAc                                                                                   >  2:95012/1‑134 (MQ=255)
                         ctAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGAt                                                                        <  1:95012/133‑1 (MQ=255)
                                     tCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGaa                                                           >  1:342018/1‑134 (MQ=255)
                                     tCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGaa                                                           >  2:860725/1‑134 (MQ=255)
                                         tgctgcAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAAt                                                          <  2:868216/131‑1 (MQ=255)
                                                                                               tGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGc  >  1:412529/1‑133 (MQ=255)
                                                                                                 gTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATcc                                                                                         <  1:674127/44‑1 (MQ=255)
                                                                                                 gTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATcc                                                                                         >  2:674127/1‑44 (MQ=255)
                                                                                                     agCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTaaaa                                                                  <  1:878507/63‑1 (MQ=255)
                                                                                                     agCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTaaaa                                                                  >  2:878507/1‑63 (MQ=255)
                                                                                                             |                                                                                                                      
CTCTTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACCTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGC  >  AM260479/3514909‑3515136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ 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
CCTCTTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACCTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGCAACTCATCCCTTGATCGCCTTGCGCTGACGC  >  AM260479/3514908‑3515167
                                                                                                              |                                                                                                                                                     
CCTCTTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCC                                                                                                                <  GWNJ‑0478:712:GW2002102894th:2:2208:4547:81891/150‑1 (MQ=60)
        tttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAG                                                                                                         <  GWNJ‑0478:712:GW2002102894th:2:2110:19830:6937/75‑1 (MQ=60)
           CCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGctgtctcttatacacatctccgagcccacgagacgg                                                                                                     >  GWNJ‑0478:712:GW2002102894th:2:1212:10428:97287/1‑114 (MQ=60)
              CAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAAACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCctgtctcttatacacatctccgagcccacgagacgg                                                                                                  >  GWNJ‑0478:712:GW2002102894th:2:2108:8771:64642/1‑114 (MQ=60)
                       CTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAAT                                                                                         >  GWNJ‑0478:712:GW2002102894th:2:1207:13634:74029/1‑150 (MQ=60)
                         GCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATC                                                                                        <  GWNJ‑0478:712:GW2002102894th:2:1106:11174:47789/149‑1 (MQ=60)
                              gacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTC                                                                                  <  GWNJ‑0478:712:GW2002102894th:2:2206:8287:72592/93‑1 (MQ=60)
                                                                                 GGGTGTAGCTTAGCCTGGTAGAGCGCTACGTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGCA                                >  GWNJ‑0478:712:GW2002102894th:2:1211:8424:97424/1‑149 (MQ=60)
                                                                                                              GTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGCAACTCATCCCTTGATCGCCTTGCGCTGACGC  >  GWNJ‑0478:712:GW2002102894th:2:1202:15307:13868/1‑150 (MQ=60)
                                                                                                              GTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGCAACTCATCCCTTGATCGCCTTGCGCTGACGC  <  GWNJ‑0478:712:GW2002102894th:2:1212:11763:43426/150‑1 (MQ=60)
                                                                                                              |                                                                                                                                                     
CCTCTTCCATTCCCCAAAAAACGCTGCTAAACTTACGTTCTTTGCTGCAGACGGTCAGACGTTTGCCAGCAAACCAAATCGGGGTGTAGCTTAGCCTGGTAGAGCGCTACCTTCGGGACGTAGAGGCCGGAGGTTCGAATCCTCTCACCCCGACCAGATTTAAAAGGCCGAATCAACGTCAGTTGGTTCGGCCTTTTGTCTTTCTGCCCCCCCTCCCCGATCCTCCGGCAACTCATCCCTTGATCGCCTTGCGCTGACGC  >  AM260479/3514908‑3515167

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