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 F11 I1 R1
|
56 |
91.5 |
3907174 |
98.4% |
3844659 |
146.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
278,744 |
+A |
intergenic (‑239/+75) |
PP_0224 ← / ← sctC |
DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 278,742 | 1 | . | A | 86.2%
| 80.9
/ 7.7
| 29 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base . (2/2); new base A (12/13); total (14/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCG‑CGAAA‑GGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGC > NC_002947_CJ‑RC/278600‑278884
|
gCTACAGCGGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTACTGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGGGCCGGGCTCTTCGC‑GGG‑T‑AAaccc < 3:447148/149‑2 (MQ=255)
cTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑Ta > 7:451902/1‑149 (MQ=255)
tGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑Ta > 4:280119/1‑148 (MQ=255)
cAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGc < 6:93497/148‑1 (MQ=255)
gACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGcc > 6:142794/1‑147 (MQ=255)
gACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCt < 6:262620/148‑1 (MQ=255)
tgCTGGTCCGGTGGTCCTGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGAt < 1:140255/148‑1 (MQ=255)
tggtccggtggtccggTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCtg < 6:274746/148‑1 (MQ=255)
tggtccggtggtccggTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCtg < 5:142794/148‑1 (MQ=255)
gtccggtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCtgt < 1:424008/147‑1 (MQ=255)
tccggtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAAACCCCTCC‑AACACAAAAGCCGCAAGATATGTGCa > 2:84158/1‑149 (MQ=255)
tatatataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCggg < 8:451902/149‑1 (MQ=255)
tatatataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCgg < 6:108383/148‑1 (MQ=255)
tataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAAACCCCAAC‑TAAACACATGCCACAAAATAAGTGGACTGTAGGAGCGGGttt > 8:496663/1‑148 (MQ=255)
taCCCTAATTATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTAc < 7:68851/148‑1 (MQ=255)
taCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTAc < 3:280119/148‑1 (MQ=255)
taCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTAc < 8:417576/148‑1 (MQ=255)
cccTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCAGTGCACTGTAGGAGCGGGTTTAACcg > 2:296622/1‑149 (MQ=255)
cTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAAACCCCACC‑AAAACACAAGCCACAAAATAAGTGGACTGTAGGAGCGGGTTTAacccc > 2:107121/1‑146 (MQ=255)
tataAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACAt < 7:441190/100‑1 (MQ=255)
tataAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACAt > 8:441190/1‑100 (MQ=255)
ttttATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAAACCCCACC‑AAAACACAATGCTCAAAAAGTGTTCACAGTAGGGGCGGGGTTTACCG‑CCAAA‑TGGCCGGaaaaagt > 2:140947/1‑144 (MQ=255)
tATGAACTAACTTTTTCGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGG‑T‑AAACCCCACC‑AACCCACAAACCACAAGAAAGGTGGACGGTAGGCCCGGGGTTAACCGCCCAAA‑GGCCCGGACCATGtt > 8:264311/1‑148 (MQ=255)
aactaactTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTa < 4:235014/107‑1 (MQ=255)
aactaactTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTa > 3:235014/1‑107 (MQ=255)
actaactTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAAACCCCGCC‑AACACAACAGCCAGAAAAAATGTGGACTGGATGAGCCGGTTTTACCG‑CGAAATGGGCCGGACAGGGTTTatcgg > 2:22579/1‑145 (MQ=255)
aaatttttttTAATTTTTATCGAGGGGGGTTTTGTTACTGGGGGGCCGGCCTCTTCGG‑GGT‑A‑AACCCCCCCCAAACCCACATCCCCAACCTTGTGCCCATTTTCGGCGGGGTTTAACCCG‑CGAAA‑GGGCCGGAACAGGTTTACTCGGAg < 8:460301/145‑1 (MQ=255)
gATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGGTT‑AAACCCCACC‑TAAACACAAGGCGCAAGATATGTGGACTGTATGAGCGGGGTTTACCG‑CGAAA‑GGGCCCGAAAAGGTTTAATCGGAGGCCCCAGTGCCGAGGGACGTTCGCAAg > 8:111201/1‑148 (MQ=255)
c‑gGG‑TAAACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCG‑CGAAA‑GGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGgcgc > 5:24131/1‑148 (MQ=255)
|
GCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AACCCGCTCC‑TACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCG‑CGAAA‑GGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGC > NC_002947_CJ‑RC/278600‑278884
|
| 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
BRESEQ :: bam2aln output
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTG > NC_002947_CJ‑RC/278599‑278886
|
CGCTACAGCGGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTACTGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGGGCCGGGCTCTTCGCGGGTAAACCCG < NB501016:282:H2V7GAFX2:2:21308:26282:20098/151‑1 (MQ=60)
GCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTAC > NB501016:282:H2V7GAFX2:4:21605:17836:5754/1‑151 (MQ=60)
GTGCTGGTCCGGTGGTCCTGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATC < NB501016:282:H2V7GAFX2:1:11208:7974:14425/150‑1 (MQ=60)
GCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGT < NB501016:282:H2V7GAFX2:3:11509:20102:18345/151‑1 (MQ=60)
GGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTG < NB501016:282:H2V7GAFX2:1:21303:22127:7717/149‑1 (MQ=60)
GTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAAACCCCCCGGCCTTCCCCTTAACCAACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAA > NB501016:282:H2V7GAFX2:4:11502:18357:5739/1‑60 (MQ=60)
ATACCCTAATTATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACC < NB501016:282:H2V7GAFX2:4:11410:5326:9761/150‑1 (MQ=60)
ATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACC < NB501016:282:H2V7GAFX2:2:21105:15222:16044/150‑1 (MQ=60)
TTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATG < NB501016:282:H2V7GAFX2:4:21603:20603:13398/102‑1 (MQ=60)
GAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAG > NB501016:282:H2V7GAFX2:2:11310:5042:18954/1‑109 (MQ=60)
AACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACAtggaatcgtttacatcggcggaatgcgcaaccacccggaagcgatgtccgaggagcttggcctgccaaacg < NB501016:282:H2V7GAFX2:3:11409:11844:4555/149‑72 (MQ=60)
TTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGG < NB501016:282:H2V7GAFX2:1:21310:18499:15670/59‑1 (MQ=60)
GCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTG > NB501016:282:H2V7GAFX2:3:11404:1801:12221/1‑151 (MQ=60)
|
CGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTG > NC_002947_CJ‑RC/278599‑278886
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
