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
A0 F0 I1 R1 155 25.8 2285122 88.0% 2010907 104.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260480 2,737,505 Δ1 bp intergenic (‑222/+22) h16_B2423 ← / ← h16_B2424 periplasmic solute binding protein/Hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604802,737,5040A.100.0% 35.3 / NA 9intergenic (‑221/+23)h16_B2423/h16_B2424periplasmic solute binding protein/Hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (3/6);  total (3/6)

GGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGT  >  AM260480/2737378‑2737610
                                                                                                                              |                                                                                                          
ggCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCAAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGACatggcgt                                                                                                      >  2:319631/1‑127 (MQ=255)
                         cAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCg                                                                           <  2:432501/134‑1 (MQ=255)
                          aGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg                                                                                               >  1:65362/1‑113 (MQ=255)
                          aGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACg                                                                                               <  2:65362/113‑1 (MQ=255)
                                             gcggcgCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCcgcg                                                       >  1:284986/1‑134 (MQ=255)
                                                              gcgcgcCAGCAAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAAt                                      <  1:319631/134‑1 (MQ=255)
                                                                               aCGCGCGTGTTGCCGCGCGGCGGGAATCATGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCcgc                                                        >  1:135124/1‑99 (MQ=255)
                                                                               aCGCGCGTGTTGCCGCGCGGCGGGAATCATGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCcgc                                                        <  2:135124/99‑1 (MQ=255)
                                                                                  cgcgTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTggcgg                  <  2:284986/134‑1 (MQ=255)
                                                                                                  gcggGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGt  <  2:913461/134‑1 (MQ=255)
                                                                                                                              |                                                                                                          
GGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGT  >  AM260480/2737378‑2737610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
TGGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGG  >  AM260480/2737366‑2737639
                                                                                                                                           |                                                                                                                                      
tttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAA                                                                                                                              <  GWNJ‑0478:712:GW2002102894th:2:1109:8789:9280/73‑1 (MQ=60)
 GGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAAC                                                                                                                             <  GWNJ‑0478:712:GW2002102894th:2:1111:2436:24255/149‑1 (MQ=60)
        attagcgagtgtctcgtgggctcggagatgtgtataagagacaggctggctGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATG                                                                                                                     <  GWNJ‑0478:712:GW2002102894th:2:1211:7682:26376/99‑1 (MQ=60)
                       GGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGctgtctc                                                                                                      >  GWNJ‑0478:712:GW2002102894th:2:1104:13070:15473/1‑143 (MQ=60)
                                          GCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGG                                                                                   >  GWNJ‑0478:712:GW2002102894th:2:1201:18061:17046/1‑150 (MQ=60)
                                                        ggcgccggagttcgcccgcatCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGC                                                                      <  GWNJ‑0478:712:GW2002102894th:2:2204:19255:79385/128‑1 (MQ=60)
                                                         ttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacatggagtcagcgacATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGC                                                                      <  GWNJ‑0478:712:GW2002102894th:2:2114:2941:18693/67‑1 (MQ=60)
                                                            ccctgattcccgcCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTctgtctcttatacacatctccgagcccacgagacactcgctaatctcgt                                                                  >  GWNJ‑0478:712:GW2002102894th:2:1110:19114:16043/14‑100 (MQ=60)
                                                            GCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtct                                                                 >  GWNJ‑0478:712:GW2002102894th:2:1106:13296:51065/1‑92 (MQ=60)
                                                                         CGCGCGCCAGCAAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGT                                                    <  GWNJ‑0478:712:GW2002102894th:2:1202:15298:36295/150‑1 (MQ=60)
                                                                            GCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCATGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCctgtctcttatacacatctcc                                                 >  GWNJ‑0478:712:GW2002102894th:2:1109:11064:23780/1‑129 (MQ=60)
                                                                                                                      CAGGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGC       >  GWNJ‑0478:712:GW2002102894th:2:2202:5394:17174/1‑150 (MQ=60)
                                                                                                                        GGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaa      >  GWNJ‑0478:712:GW2002102894th:2:1111:8591:77003/1‑67 (MQ=60)
                                                                                                                        GGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCC      >  GWNJ‑0478:712:GW2002102894th:2:1210:3528:63552/1‑149 (MQ=60)
                                                                                                                        GGGACGGGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCC      >  GWNJ‑0478:712:GW2002102894th:2:2114:3407:46556/1‑149 (MQ=60)
                                                                                                                              GGAGTCAGCGAC‑ATGGCGTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGctgtctcttatacacatctccgagcccacg  >  GWNJ‑0478:712:GW2002102894th:2:2102:11382:59527/1‑117 (MQ=60)
                                                                                                                                           |                                                                                                                                      
TGGGCCGGTGCCGGCGTGTAGGTGGCCTGCGCATGGCCAGCGGCCGGCAGGGCAAGCGCGGCGCCCGCGAGGGCGCGCGCCAGCCAGCGCCACGCGCGTGTTGCCGCGCGGCGGGAATCAGGGACGGGAGTCAACGACAATGGCTTCAAACGGTTCATGTTTCAGGGAGTCGAGGGCGCGCCTGGAGCCGCGGCAAGGCCAACGGCAATGGCGGGCGCCTGGGTGGCGGCGGGCAGCGTGGCAGTGGCCGGGGCCGCGGGCGCCACGGCCATGG  >  AM260480/2737366‑2737639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑