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 |
|
A0 F0 I1 R1
|
52 |
69.5 |
2964196 |
98.4% |
2916768 |
145.9 |
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 | 83.3%
| 60.3
/ 8.4
| 24 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base . (3/1); new base A (2/18); total (5/19) |
| Fisher's exact test for biased strand distribution p-value = 1.84e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGTTTA‑CCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAA > NC_002947_CJ‑RC/278595‑278857
|
aTGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑t > 4:258906/1‑148 (MQ=255)
gTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑AGG‑T‑aaa > 8:162982/1‑148 (MQ=255)
cAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTc < 2:21027/149‑1 (MQ=255)
gCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCt < 6:97353/149‑1 (MQ=255)
aTCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTac < 4:344363/147‑1 (MQ=255)
aCAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGc < 1:333127/149‑1 (MQ=255)
gACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTc < 7:206506/149‑1 (MQ=255)
cGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCaa < 5:149512/149‑1 (MQ=255)
gtgtGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAg < 3:9701/149‑1 (MQ=255)
tgCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGTAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGAt < 7:317885/148‑1 (MQ=255)
cTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCt < 7:290488/148‑1 (MQ=255)
tggtccggtggtccggTATATATACCCTAATGATTTATAAAATTTTTATGAACT‑ACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGG‑T‑AA‑‑ACCCCTCCGAGACCCAAGACGCAAGATAtgtg > 8:357891/1‑149 (MQ=255)
gtccggtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCtgt < 6:198825/147‑1 (MQ=255)
gtggtccggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGt < 4:284030/149‑1 (MQ=255)
cggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAg < 1:106815/148‑1 (MQ=255)
cggtATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGc < 2:119778/149‑1 (MQ=255)
taCCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGTTTA‑c < 6:230037/148‑1 (MQ=255)
cccTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGTTTA‑ccc < 5:233863/148‑1 (MQ=255)
gATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGGTT‑AA‑‑CCCGCGCCAAAACAAATTCCGCAAGATGTGTGCACGGTAGGAGC‑GGGTTTT‑ACCGCGAAAgg > 8:131166/1‑149 (MQ=255)
ataAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGt > 4:151308/1‑130 (MQ=255)
ataAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGt < 3:151308/130‑1 (MQ=255)
aactaactTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGGTT‑AA‑‑ACCCCACCAACACAAAATCCGCAAGATAAGTGGACAGTATGAGCGGGGTTTA‑CCC‑CGAAAAGGGCGGGACAGGgtttatag > 8:186761/1‑144 (MQ=255)
aaGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑AGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGTTTA‑CCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTgc < 7:162982/149‑1 (MQ=255)
tttGTTACCGGGGGGCCGGGCTC‑TCGG‑GGG‑T‑AAACCCCGCCCAAACACCCCCCCCTACAGTTGTTTGCATTGTCGGCG‑‑GGGTTTACCCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGaa < 2:275363/148‑1 (MQ=255)
gc‑gGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATc > 2:351277/1‑37 (MQ=17)
gc‑gGG‑TAAA‑‑CCCGCTCCTACACACATGCCTCAAGATc < 1:351277/37‑1 (MQ=17)
|
ATGTCGCTACAGCTGATCGCGACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGC‑GGG‑T‑AA‑‑CCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC‑GGGTTTA‑CCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAA > NC_002947_CJ‑RC/278595‑278857
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAA > NC_002947_CJ‑RC/278615‑278889
|
GACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCC < NB501016:282:H2V7GAFX2:1:21306:19108:1768/151‑1 (MQ=60)
AGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCA < NB501016:282:H2V7GAFX2:4:21403:19176:10704/151‑1 (MQ=60)
ACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAG < NB501016:282:H2V7GAFX2:3:11605:3962:11379/151‑1 (MQ=60)
CGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGA < NB501016:282:H2V7GAFX2:2:11102:21999:20080/151‑1 (MQ=60)
GTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGTAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATC < NB501016:282:H2V7GAFX2:4:21511:3742:18185/150‑1 (MQ=60)
GCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTG < NB501016:282:H2V7GAFX2:4:21506:9652:16710/150‑1 (MQ=60)
CCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGC < NB501016:282:H2V7GAFX2:1:11208:2692:17558/150‑1 (MQ=60)
ACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCG < NB501016:282:H2V7GAFX2:3:21410:6927:4690/150‑1 (MQ=60)
TATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTT < NB501016:282:H2V7GAFX2:2:11306:2065:6012/132‑1 (MQ=60)
GAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCAGGTAAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCG < NB501016:282:H2V7GAFX2:4:11607:21481:5455/151‑1 (MQ=60)
CGCGGGTAAACCCGCTCCTACACACATGCCTCAAGATCT < NB501016:282:H2V7GAFX2:1:21309:7226:15203/39‑1 (MQ=20)
gtaAACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAA > NB501016:282:H2V7GAFX2:2:21211:15226:11813/4‑150 (MQ=60)
|
GACAGACGTGTGCTGGTCCGGTGGTCCGGTATATATACCCTAATGATTTATAAAATTTTTATGAACTAACTTTTTGGAATATTTATAGAAGGGGGATTTGTTACAGAGGTGCCGGGCTCTTCGCGGGT‑AACCCGCTCCTACACACATGCCTCAAGATCTGTGCACTGTAGGAGCGGGTTTACCCGCGAAAGGGCCGGAACAGGTTTACTCGGAGGCCGCAGTCCCGAGGAACTTGCGCAAGAACTGCCGCGTACGCTCTTCCTTCGGCGCTGCAA > NC_002947_CJ‑RC/278615‑278889
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
