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 F2 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 539,975 A→G D258D (GAT→GAC)  allC ← allantoate deiminase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273539,9750AG88.9% 40.0 / ‑0.1 18D258D (GAT→GAC) allCallantoate deiminase
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base G (13/3);  total (15/3)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-01

ACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT  >  NZ_CP009273/539902‑540061
                                                                         |                                                                                      
aCGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCg                                                                        >  2:772583/1‑90 (MQ=255)
               gCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACt                                                         >  2:109324/1‑90 (MQ=255)
                         tACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAAt                                               >  1:281913/1‑90 (MQ=255)
                         tACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAAt                                               >  2:724494/1‑90 (MQ=255)
                         tACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAAt                                               >  2:709638/1‑90 (MQ=255)
                               aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt                                         >  2:311496/1‑90 (MQ=255)
                               aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt                                         >  2:647382/1‑90 (MQ=255)
                               aTTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACt                                         >  1:804719/1‑90 (MQ=255)
                                 tCGGGCGGGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGa                                       <  2:386249/90‑1 (MQ=255)
                                   gggCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGaaa                                     >  1:217970/1‑90 (MQ=255)
                                                    gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  2:392229/1‑90 (MQ=255)
                                                    gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    <  2:607174/90‑1 (MQ=255)
                                                    gCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  2:14196/1‑90 (MQ=255)
                                                    gCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCacg                    >  2:310374/1‑90 (MQ=255)
                                                              aGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAAccc          >  2:411114/1‑90 (MQ=255)
                                                                    aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc    >  2:211683/1‑90 (MQ=255)
                                                                    aGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGc    >  2:714319/1‑90 (MQ=255)
                                                                      cGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCgt  <  2:52784/90‑1 (MQ=255)
                                                                         |                                                                                      
ACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAAGCGTAAACTGTATCACGACGATAACCCATCGGCGT  >  NZ_CP009273/539902‑540061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGACAATCAATGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAA  >  NZ_CP009273/539886‑540026
                                                                                         |                                                   
gagatcctctctggtctcgtgggctcggagatgtgtataagagacagATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCC                                           <  SRR3722079.769558/53‑1 (MQ=60)
                               GCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAAT            >  SRR3722079.284255/1‑100 (MQ=60)
                                     CATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACT      >  SRR3722079.813353/1‑100 (MQ=60)
                                         TACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGGTCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAA  >  SRR3722079.219824/1‑100 (MQ=60)
                                                                                         |                                                   
CGACAATCAATGGTGAACGTGGTTTTACCCGGCACCACATTTACCGTATTCGGGCGCGGCTCTACTTTGCCAAAGGTCAGAACCAGCGGATCGCCCATCCTTTTCGCTTTTTCGACCGACTGATGGCAAATGCGACTGAAA  >  NZ_CP009273/539886‑540026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑