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 F11 I1 R1 56 79.5 3383150 98.4% 3329019 146.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 1,932,640 +C intergenic (‑107/+43) rluA ← / ← minE bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC1,932,6381.C92.9% 41.4 / ‑2.2 14intergenic (‑105/+45)rluA/minEbifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (12/1);  total (13/1)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

AGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAT  >  NC_002947_CJ‑RC/1932506‑1932779
                                                                                                                                      |                                                                                                                                             
agagGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGGCAGCCCCCGCCGACAAAGGCTAATCCGCCCCCGGAGGAGCGGGCGTGG‑CCGAGGAGGGcggg                                                                                                                                 >  6:192506/1‑145 (MQ=255)
                                                                                         cccGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAg                                       >  3:403241/1‑149 (MQ=255)
                                                                                          ccGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGc                                      >  8:383652/1‑149 (MQ=255)
                                                                                           cGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCt                                     >  5:213093/1‑149 (MQ=255)
                                                                                                 tACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGatat                               >  4:249255/1‑149 (MQ=255)
                                                                                                  aCAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATcc                                                                                         >  5:97877/1‑90 (MQ=255)
                                                                                                  aCAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATcc                                                                                         <  6:97877/90‑1 (MQ=255)
                                                                                                    aaaGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCACGGTGATGTTCATCTCCAGAATCGAGCAGCTGCCAAGGTTTTCCAGCTCGAAATGc                             >  6:36457/1‑148 (MQ=38)
                                                                                                     aaGGATATGCGTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGca                            >  7:47272/1‑148 (MQ=255)
                                                                                                               gTCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCAAGCTCGAAATGCACATCAACGTTg                 >  4:114717/1‑149 (MQ=39)
                                                                                                                tCCCCTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGc                >  1:221377/1‑149 (MQ=255)
                                                                                                                  cccTGTAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGcc               >  6:87113/1‑148 (MQ=255)
                                                                                                                       tAGGAGCGGGC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGtt         >  8:223262/1‑149 (MQ=255)
                                                                                                                              gggC‑TTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACatat  >  1:291606/1‑149 (MQ=255)
                                                                                                                                      |                                                                                                                                             
AGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGC‑TTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAT  >  NC_002947_CJ‑RC/1932506‑1932779

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