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 F18 I1 R1 59 77.7 3515218 98.5% 3462489 145.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 3,951,161 A→T intergenic (‑125/+70) PP_3486 ← / ← PP_3487 cytochrome c/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC3,951,1610AT100.0% 45.7 / NA 15intergenic (‑125/+70)PP_3486/PP_3487cytochrome c/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (13/2);  total (13/2)

GGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCG  >  NC_002947_CJ‑RC/3951079‑3951302
                                                                                  |                                                                                                                                             
ggCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGGGACGCACGGCCGCTCCCACACAAGCGGATGCCTCAGAGGCCAAGTCCCCAGGCGGCGCATgc                                                                             >  2:236359/1‑148 (MQ=255)
                 gggCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGc                                                              >  4:263480/1‑147 (MQ=255)
                       cgcAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCACGCGGCCCAAGATACTCACCCACCGGCCAGCGGCt                                                      >  4:360561/1‑149 (MQ=39)
                         cagcagCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTgg                                                    >  4:166646/1‑149 (MQ=255)
                                            aGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCCCCCCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGGCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCAAGCGCt                                 >  3:335651/1‑149 (MQ=255)
                                            aGCTCAAGCGCAGAAAGAGGGGAGCGCAGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATCCCACAGAGGCCAAATCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCAGGGTCAACAGCTGCATGCGCt                                 >  7:212064/1‑149 (MQ=255)
                                               tCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTggg                              >  2:108417/1‑149 (MQ=255)
                                                 aaGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCCCAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGCCCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGc                             >  5:21140/1‑148 (MQ=255)
                                                         aaaGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATcgccgc                    >  2:9860/1‑149 (MQ=255)
                                                           agagGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTg                  >  7:72946/1‑149 (MQ=255)
                                                               gggAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCgg              <  3:263480/149‑1 (MQ=255)
                                                                ggAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCACTGGGCAATCGCCGCTGGCGGt             >  7:334600/1‑149 (MQ=255)
                                                                    cgcTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCAt         <  3:166646/149‑1 (MQ=255)
                                                                      cTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATcc       >  8:223837/1‑149 (MQ=255)
                                                                            gcTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCg  >  2:38347/1‑148 (MQ=255)
                                                                                  |                                                                                                                                             
GGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCG  >  NC_002947_CJ‑RC/3951079‑3951302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A