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
A3 F38 I1 R1 54 64.3 2734350 98.3% 2687866 146.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 5,558,423 +GCC intergenic (‑84/+87) PP_4887 ← / ← PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC5,558,4231.G87.5% 16.5 / ‑2.2 8intergenic (‑84/+87)PP_4887/PP_4888hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base G (2/5);  total (2/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.09e-01
*NC_002947_CJ‑RC5,558,4232.C87.5% 19.0 / ‑2.6 8intergenic (‑84/+87)PP_4887/PP_4888hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (2/5);  total (2/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01
*NC_002947_CJ‑RC5,558,4233.C87.5% 19.4 / ‑2.6 8intergenic (‑84/+87)PP_4887/PP_4888hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (2/5);  total (2/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

GCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCC  >  NC_002947_CJ‑RC/5558311‑5558552
                                                                                                                    |||                                                                                                                                 
gaagtgATTAGTGGGGCGTACTTGAGCAACTCTTTTTGTCATGTTTCGCCGAATGATTAGCAACACCGCTCTGGTGTGGGTGGGGCCTTGTGTCGCTAACGGGCCGAATT‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg                                                                                                  <  8:182861/144‑1 (MQ=255)
 cAGCGATTCGTCGGCCGGACATGAGCAACTCCTTTTGTCATGTGCCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCGAACGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTggg                                                                                                 <  2:110860/149‑1 (MQ=37)
          tgcGGGCGTAAATGACCAACTCCTTTTGTCATGTGTCGCCTACAGATTAGCAACACCGCTCGGGTGTGGTCGCGGCCTTGTGGCGATAATGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt                                                                                         <  2:270486/146‑1 (MQ=255)
            cGGCCGGACATCACCAACTCCTTTTGTCTTGTGCCCCCGACAGCATACCAACCCCGCACCGGTGTGGGCGCGCCCTGGTGCCGCTAACGGGCCCCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCa                                                                                      <  6:191044/149‑1 (MQ=255)
                    cATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc                                                                              <  2:198735/149‑1 (MQ=255)
                                                ccGACTCCATCGCAACACCGCGCCGGGGGGGGTGGGGCCTTGTGACGCCAATGGGCCGATTAGTGGCC‑‑‑CCGGAAATTACCGCGTGTTTCAACCAAACCTGGGGCTGCTAGCCCGCCGTTCGGCTAAACAAGGCCCACAAAGGACCgcgc                                                  <  8:49401/149‑1 (MQ=255)
                                                                                               cgAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTACGCGTGTATGCACCAAACCTGGGGCTGCTATGCCGCCCTTTAGCGACACACGGCCCACAAAGGACCGCGCAGGCTTCAGTCCCGGAACTGGCCCAGGCTGGCGCGCAGCAGAgccgc   >  8:3458/1‑149 (MQ=255)
                                                                                                gAAAGGGCCGCATA‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCGTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgcc  >  7:201873/1‑149 (MQ=255)
                                                                                                                    |||                                                                                                                                 
GCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATA‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCC  >  NC_002947_CJ‑RC/5558311‑5558552

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A