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 F48 I1 R1
|
58 |
71.3 |
3054194 |
98.3% |
3002272 |
146.3 |
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 | 85.2%
| 75.0
/ 8.4
| 27 | 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 (5/18); total (7/20) |
| Fisher's exact test for biased strand distribution p-value = 2.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGT‑AACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA‑CCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGC > NC_002947_CJ‑RC/278595‑278884
|
aTGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGt < 2:225183/148‑1 (MQ=255)
tCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGT‑aaac > 5:710/1‑147 (MQ=255)
cAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTc < 1:298318/149‑1 (MQ=255)
gCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCt < 4:106254/149‑1 (MQ=255)
cTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTa < 3:23708/149‑1 (MQ=255)
cgcgACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGT‑AAacc < 6:168205/136‑1 (MQ=255)
cgcgACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGT‑AAacc > 5:168205/1‑136 (MQ=255)
gACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATg < 3:62209/149‑1 (MQ=255)
aGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCt < 1:197883/149‑1 (MQ=255)
cGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCaa < 4:156117/149‑1 (MQ=255)
cTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGCGGGGT‑AAACCC‑CGCCAACACCCCAGCCGCAAGAtgtg > 5:165664/1‑149 (MQ=255)
tggtccggtggtccggTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCtgt > 3:177063/1‑149 (MQ=255)
tggtccggtggtccggTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCtgt < 6:12487/149‑1 (MQ=255)
gtccggtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCtgt < 6:956/147‑1 (MQ=255)
tccggtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCa < 5:94095/149‑1 (MQ=255)
gtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGt < 5:232906/149‑1 (MQ=255)
gtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCgg < 3:309743/149‑1 (MQ=255)
tatatataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCgg < 3:225806/148‑1 (MQ=255)
atatataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGt > 4:202730/1‑149 (MQ=255)
tatataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGt < 4:177063/148‑1 (MQ=255)
tatataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGt < 6:710/148‑1 (MQ=255)
ataCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA‑c < 3:202730/149‑1 (MQ=255)
taCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA‑cc < 5:355579/149‑1 (MQ=255)
ccTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA‑CCcgc < 1:14380/149‑1 (MQ=255)
tAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCtgt < 5:292171/122‑1 (MQ=255)
tAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCtgt > 6:292171/1‑122 (MQ=255)
aTGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGTAAACCCG‑CTCCTac > 6:191594/1‑100 (MQ=255)
ttttATAG‑ATGGGGTTTTGTTACCCGCGGTGCCGGGCTTTCCGC‑GGTT‑AACCCGTCTCAAACACACATCCCACAAGATCTGTGCACTGTCGGCG‑GGTTTTACCCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGa < 6:71526/147‑1 (MQ=255)
gc‑gGGTAAACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA‑CCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGgcgc > 1:55913/1‑149 (MQ=255)
|
ATGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTA‑CAGAGGTGCCGGGCTCTTCGC‑GGGT‑AACCCG‑CTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTA‑CCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGC > NC_002947_CJ‑RC/278595‑278884
|
| 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
BRESEQ :: bam2aln output
GTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAACAGG > NC_002947_CJ‑RC/278597‑278894
|
GTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AAACC > NB501016:282:H2V7GAFX2:3:11401:8526:3859/1‑151 (MQ=60)
ACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCC < NB501016:282:H2V7GAFX2:1:21208:5718:2942/151‑1 (MQ=60)
GCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTAC < NB501016:282:H2V7GAFX2:2:11105:21069:12511/151‑1 (MQ=60)
acgagatttctgaatgtgactggagttcagacgttgctcttccgatCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACA < NB501016:282:H2V7GAFX2:3:11612:8115:6773/104‑1 (MQ=60)
TCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCC > NB501016:282:H2V7GAFX2:3:11608:19509:3695/1‑138 (MQ=60)
CGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGC < NB501016:282:H2V7GAFX2:2:11112:12690:18312/151‑1 (MQ=60)
CAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTC < NB501016:282:H2V7GAFX2:1:21101:7218:3333/151‑1 (MQ=60)
CTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTG > NB501016:282:H2V7GAFX2:2:11309:4672:15823/1‑151 (MQ=60)
GTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCAC < NB501016:282:H2V7GAFX2:3:11507:6236:1269/151‑1 (MQ=60)
GGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTA < NB501016:282:H2V7GAFX2:3:21408:20081:15634/151‑1 (MQ=60)
GGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGG < NB501016:282:H2V7GAFX2:2:21301:4891:13686/151‑1 (MQ=60)
GTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGG < NB501016:282:H2V7GAFX2:2:21107:22435:6233/150‑1 (MQ=60)
AATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACC < NB501016:282:H2V7GAFX2:2:21102:15285:10224/151‑1 (MQ=60)
ATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCC < NB501016:282:H2V7GAFX2:3:21607:2707:19962/151‑1 (MQ=60)
CCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCG < NB501016:282:H2V7GAFX2:1:11103:20745:9435/151‑1 (MQ=60)
CTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTG < NB501016:282:H2V7GAFX2:3:21508:1999:10294/124‑1 (MQ=60)
TGCCGGGCTCTTCGCGGGTAAACCCGCTCATACACACATGCCTCAAGATGTGTTCACAGTAGGAGAGGGTTTACGTGCGAAAGGGCCGGAACAGGTTTACTCGCAGGCAGCAGTCCAGATGAACTTGCGCAAGAACTTCCGCGTACGCTCT > NB501016:282:H2V7GAFX2:3:21402:2693:10365/1‑151 (MQ=60)
CGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCT > NB501016:282:H2V7GAFX2:1:11110:22500:13477/1‑151 (MQ=60)
ACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAACAGG > NB501016:282:H2V7GAFX2:3:21503:3606:5161/1‑151 (MQ=60)
|
GTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAAACAGG > NC_002947_CJ‑RC/278597‑278894
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
