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 F44 I1 R1 56 64.5 2756482 98.4% 2712378 146.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 4,586,137 2 bp→TC intergenic (+113/+101) PP_4061 → / ← PP_4063 hypothetical protein/long‑chain fatty acid‑‑CoA ligase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,586,1370CT100.0% 45.6 / NA 15intergenic (+113/+102)PP_4061/PP_4063hypothetical protein/long‑chain fatty acid‑‑CoA ligase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (1/14);  total (1/14)
*NC_002947_CJ‑RC4,586,1380TC100.0% 47.6 / NA 15intergenic (+114/+101)PP_4061/PP_4063hypothetical protein/long‑chain fatty acid‑‑CoA ligase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (1/14);  total (1/14)

CCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAA‑ACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTA  >  NC_002947_CJ‑RC/4586000‑4586209
                                                                                                                                         ||                                                                          
ccAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑Ac                                                                 >  2:155212/1‑149 (MQ=255)
      gCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTc                                                           <  5:177459/149‑1 (MQ=255)
          ccGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTAc                                                       <  7:335914/149‑1 (MQ=255)
            ggTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCa                                                     <  3:194046/149‑1 (MQ=255)
                  ggCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAggggca                                               <  6:200855/149‑4 (MQ=39)
                    cTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGA‑ccgt                                            <  2:86098/149‑4 (MQ=39)
                       aaGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTTCTCGATTGTATGGTTGAGGATGACCGGGTGCTTGTCAAGGGGAAGATCTTGGATTGATCGGGCCGGCCTCTTCGC‑GGGAATACCCGCTCCTACCAgggtgcgttc                                           <  6:239203/148‑8 (MQ=255)
                          ggTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGc                                       <  6:66808/149‑1 (MQ=39)
                                     gCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATgcgg                            <  2:239776/149‑1 (MQ=39)
                                             gTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGccc                    <  2:192736/149‑1 (MQ=39)
                                                  cAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGt               <  8:43132/149‑1 (MQ=39)
                                                   aGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTa              <  2:113136/149‑1 (MQ=39)
                                                             cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGt     <  3:37483/148‑1 (MQ=38)
                                                             cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCGCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCGGTGAATGCGGCGCTGCCCCTGGTAGGAGCgg       <  2:291659/146‑1 (MQ=38)
                                                               ctgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAA‑ACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTa  <  1:155212/149‑1 (MQ=38)
                                                                                                                                         ||                                                                          
CCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAA‑ACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTA  >  NC_002947_CJ‑RC/4586000‑4586209

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

GATK/CNVnator alignment

N/A