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
A5 F13 I0 R1 213 60.4 2554362 98.6% 2518600 147.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 3,447,291 T→G 29.3% A19A (GCT→GCG)  PP_5556 → bacteriophage lysis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC3,447,2910TG29.3% 25.5 / 5.4 30A19A (GCT→GCG) PP_5556bacteriophage lysis protein
Reads supporting (aligned to +/- strand):  ref base T (16/4);  new base G (4/5);  total (21/9)
Fisher's exact test for biased strand distribution p-value = 8.80e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGAT  >  NC_002947_CJ‑RC/3447145‑3447438
                                                                                                                                                  |                                                                                                                                                   
cATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCGACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTg                                                                                                                                                    <  3:219143/148‑1 (MQ=255)
cATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTgg                                                                                                                                                   <  6:111778/149‑1 (MQ=255)
               cAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGc                                                                                                                                    >  1:242937/1‑149 (MQ=255)
                         aaTGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCCGGCAGCCTGGGTGTgg                                                                                                                          >  5:95234/1‑149 (MQ=255)
                                 tAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTTGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCaa                                                                                                                  >  8:285747/1‑149 (MQ=255)
                                              gaggaTCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCAGGCGGGGTGTGGGAGGCCAACGCCGATATGgcg                                                                                                     >  8:278980/1‑149 (MQ=255)
                                                      cAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCACCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGc                                                                                             >  6:31710/1‑149 (MQ=255)
                                                       aaGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCGGGCGGCGCCCGGGCCGCCAGGGTGTGGCAGGCCAACCCCTATAAGGCGCAGCACgtt                                                                                            >  5:247555/1‑147 (MQ=255)
                                                          gCCCTCTACACGCGCGCGCGCGTGGTTCTGCTGTGAGCGTTGGGGCCACCCGCGGGGTCGCCGTGGCGCTGCTGCGGGCCGCCAGCGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGAt                                                                                         <  6:173046/149‑1 (MQ=255)
                                                           cccTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCACCGCAGGCGGCGCCCCGGCCGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCACCACGCTGAt                                                                                         >  5:173046/1‑148 (MQ=255)
                                                                tACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGcc                                                                                   >  7:300076/1‑149 (MQ=255)
                                                                   acgcgagcgCTCTGGGTGCTGCTGGGTGCGTTTGGGCCTCCGGCGGGTTCGGTGTGCTGGTGGTGCTGGCCGCGTTGGGTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGAt                                                                                <  6:295075/147‑1 (MQ=255)
                                                                   acgcgagcgCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGAt                                                                                <  8:54437/147‑1 (MQ=255)
                                                                    agcgagcgCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCGGGCGGCGCCCGGGCCGCCGGGGTGTGGCAGGCCAACGCCGATAAgg                                                                                                       >  5:77112/1‑125 (MQ=255)
                                                                     gcgagcgCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCACCGCTGGCGGCGCCCGGGCCGCCAGGGGGTGGCAGGCCCACGCCGATAAGGCGCAGCTCGCGGATCAGGCCGATGa                                                                              >  3:190892/1‑149 (MQ=255)
                                                                             tCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGCTGACTTCGGc                                                                       >  3:260087/1‑148 (MQ=255)
                                                                               gAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCCGCCTGGGGGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAg                                                                    >  7:5149/1‑149 (MQ=255)
                                                                                       gcAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCCCGCTGGCGGCGCCCCGGCAGCCTGGGTGTGGCAGGCCAACCCCTATAATGCGCAGCACGCTGATCAGGCCGATGACTTCGGTAAGCAGTTGGc                                                            >  4:269411/1‑149 (MQ=255)
                                                                                             aGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCCGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGgag                                                        >  4:124864/1‑147 (MQ=255)
                                                                                                gcTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCACCGCGGGGGGCGGCCGGGCCGCCGGGGGGTGGCGGGCCAACCCCGATAAGGCGCCGCTCGGTGGTCAGGCCGGTGTCTTAGGCGAGCAGGTGGGGGGGAAGGa                                                   >  2:245764/1‑149 (MQ=255)
                                                                                                  ttGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCGGGGTGTGGCAGGCCAACGCCGATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATc                                                 >  6:94593/1‑149 (MQ=255)
                                                                                                  tggggCCCCCCGCGTGGGCGCGGGGGCGGTGCTGCGGGCCGCCTGGGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATc                                                 <  2:257682/147‑1 (MQ=255)
                                                                                                  tggggCCACCGGCGGGGGCGCGGTGGGGTGGCTGGGGGCGGCCCGGGGGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATc                                                 <  2:262184/147‑1 (MQ=255)
                                                                                                      gCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCCGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCGCGCTGATCAGGCCGCTGGCTTCGGCAAGCAGTTGGCGGAGAAGGATggcgc                                             >  2:293204/1‑149 (MQ=255)
                                                                                                       ccACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATcgcgcg                                            >  6:153271/1‑149 (MQ=255)
                                                                                                                             gctgctgctGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCGGGGGGTGGCAGGCCAACCCCAATAAGGCGCAGCTCGCTGATCAGGCCGCTGACTTCCGCAAGCCGATGGCCGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGaacg                      >  2:121867/1‑147 (MQ=255)
                                                                                                                               tgctgctgGCCCCCCGCGCTGGCGGCGCCCGGGCACCCTGGGTGGGGGAGGCCCACCCCCAAAAGGCGCCGGTGGGTGTTAAGGGCGCAGACTTAGGGTAGGAGGTGTCGGAGAAGGATGGCCGGCCAGGTCGGGAGCGGGAGACGGCt                    >  2:145085/1‑149 (MQ=255)
                                                                                                                                gcggcgggCCGCCGGCGCGGCCCGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTg                   <  1:245764/143‑1 (MQ=255)
                                                                                                                                   gcggcccgcccgcGCGGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgcag                <  3:22497/144‑1 (MQ=255)
                                                                                                                                    ctgGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTgcag                >  2:43262/1‑148 (MQ=255)
                                                                                                                                                  tGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGAt  >  3:175249/1‑148 (MQ=255)
                                                                                                                                                  |                                                                                                                                                   
CATCCTGGCGATCACCAAACGTATCAATGGTGGTAGCAACGGTCTGGAGGATCGCAAGGCCCTCTACAAGCGAGCGCTCGAGGTGCTGCAGTGAGCGCTTGGGCCACCCGCCTGGTCGCCGTGGCGCTGCTGCTGGCCGCCAGCGCTGGCGGCGCCCGGGCAGCCTGGGTGTGGCAGGCCAACGCCTATAAGGCGCAGCTCGCTGATCAGGCCGATGACTTCGGCAAGCAGTTGGCGGAGAAGGATCGCGCGCACGGTCTGGAGCGGGAGAAGGCTGCAGCAGCAGCGCTCGAT  >  NC_002947_CJ‑RC/3447145‑3447438

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A