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 F53 I1 R1
|
62 |
81.2 |
3465250 |
98.6% |
3416736 |
145.3 |
Breseq alignment
BRESEQ :: Evidence
|
| 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 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,932,638 | 1 | . | C | 88.9%
| 52.8
/ 0.3
| 18 | intergenic (‑105/+45) | rluA/minE | bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base C (15/1); total (17/1) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAG‑CGGGCTTG‑C‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATT > NC_002947_CJ‑RC/1932502‑1932780
|
tCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCCAACCCCCACCAACAAAAGATATTGGGGCCCAGTATGAGCCGGGGTTC‑C‑cgcgcacgg > 2:74695/1‑143 (MQ=255)
cAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGttt > 2:4347/1‑148 (MQ=255)
ccGCTCCTACAAAGGATATGCGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAg > 1:19757/1‑148 (MQ=255)
aCAAAGGATATGCGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGatat > 1:315463/1‑148 (MQ=255)
cAAAGGATATGCGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATg > 3:273757/1‑148 (MQ=255)
ggATATGCGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGcac > 4:244954/1‑147 (MQ=255)
gATATGCGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCAcat < 4:273757/148‑1 (MQ=255)
cGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGt > 1:297172/1‑148 (MQ=255)
cGTCCCCTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGATTTTCCAGCTCGATATGCACATCATCGt > 5:85412/1‑148 (MQ=255)
cTGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGa > 1:2571/1‑148 (MQ=255)
cTGTAGGAG‑CGGGCTTG‑CACGCGAAGGGCTGCAAGGCAGCACCAAATTGTCGACTACGCGGATCAGCGCTCCGGGAGGGTGATGTTCAGCACCAGAATAGAGCAGCTGCCCTGGTTATCCAGCTCGATATGCACATAATCGTTGCCg > 2:38372/1‑147 (MQ=255)
tGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAt > 4:394704/1‑148 (MQ=255)
tGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAt > 4:401175/1‑148 (MQ=255)
tGTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAt > 7:239806/1‑148 (MQ=255)
gTAGGAG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATg > 1:11082/1‑148 (MQ=255)
aG‑CGGGCTTGCC‑CGCGAAGGGCTGCAAGGGAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGtt > 8:61539/1‑145 (MQ=255)
ggCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACatat > 5:117303/1‑148 (MQ=255)
gCTTGCC‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAtt > 5:52600/1‑148 (MQ=255)
|
TCGAAGAGGATCTGGACATTCGACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAG‑CGGGCTTG‑C‑CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATT > NC_002947_CJ‑RC/1932502‑1932780
|
| 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
GACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCGGATC > NC_002947_CJ‑RC/1932523‑1932788
|
ccccggccttgtgcgggcctaacaaaagctcatcccccggggggggcgtttggcgcggcgggcggcccccccccgtcaaaaaaaacttaaggccgcccgctggggcggggggcggccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCG < NB501016:282:H2V7GAFX2:3:21504:24037:14333/34‑1 (MQ=33)
ccccctcactcacacaaaacaaactcagcctcccggggggggggcgcgggcgcgcggcggggcggccccccccccccatcatccccgtcccgcgccgcggggggggcggccccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCG < NB501016:282:H2V7GAFX2:2:21106:8871:17810/34‑1 (MQ=33)
gttacacaaaaaaacccaaaaccggggggggcggtttggcgccctggcggggcaccccccccacaaaaaacttatctgggccccgtttcggggggggctgccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGC < NB501016:282:H2V7GAFX2:4:21403:13012:17075/49‑1 (MQ=60)
ccccccccggggggcggggtggggcgcgccgcgccggccccaccccccccaaaaccccccgccgcgccccgggggggggggggccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGT < NB501016:282:H2V7GAFX2:2:11110:22851:10612/62‑1 (MQ=60)
ggcgtctggcgcgccgcctgccccccccgcccgtaaccaacacgataaacccccagcggtcggggcggcacccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTCATGTTCAGCTCCA < NB501016:282:H2V7GAFX2:2:21101:10454:1829/76‑1 (MQ=60)
cctaccccccggggcgccaccgccccaacaaaaactttatgcgccccccctctggggggggccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAG < NB501016:282:H2V7GAFX2:3:21512:2671:12080/84‑1 (MQ=60)
ccctcccgctacacaatctgcgtggtgccggcggggtggggggggcggcccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTT < NB501016:282:H2V7GAFX2:1:21306:10277:7960/100‑1 (MQ=60)
GCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGC > NB501016:282:H2V7GAFX2:1:11103:21346:18815/1‑151 (MQ=60)
CTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATG > NB501016:282:H2V7GAFX2:1:21203:24445:19696/1‑151 (MQ=60)
TACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGC > NB501016:282:H2V7GAFX2:2:21110:7683:12024/1‑151 (MQ=60)
aaaactaatcgcgcccccttggcggggggggcgcccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCA < NB501016:282:H2V7GAFX2:4:21607:13468:3862/115‑1 (MQ=60)
TGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTT > NB501016:282:H2V7GAFX2:1:21112:1172:18933/1‑151 (MQ=60)
TGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGATTTTCCAGCTCGATATGCACATCATCGTT > NB501016:282:H2V7GAFX2:3:11503:18481:8791/1‑151 (MQ=60)
CCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAT > NB501016:282:H2V7GAFX2:1:11101:24738:8689/1‑151 (MQ=60)
CCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATG > NB501016:282:H2V7GAFX2:4:21403:24240:14273/1‑151 (MQ=60)
CTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGT > NB501016:282:H2V7GAFX2:1:11102:21987:13643/1‑151 (MQ=60)
tttggggggggctcccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTT < NB501016:282:H2V7GAFX2:3:11510:9949:15269/134‑1 (MQ=60)
gggggggggttgccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCA < NB501016:282:H2V7GAFX2:4:21609:25520:9683/136‑1 (MQ=60)
ggggggggcggccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACA < NB501016:282:H2V7GAFX2:3:11506:6940:13806/138‑1 (MQ=60)
CGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATT > NB501016:282:H2V7GAFX2:3:11508:16043:10692/1‑151 (MQ=60)
GGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT > NB501016:282:H2V7GAFX2:3:11409:14218:19452/1‑151 (MQ=60)
ccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGC < NB501016:282:H2V7GAFX2:3:11412:5918:17258/145‑1 (MQ=60)
tgccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCG < NB501016:282:H2V7GAFX2:4:11505:1954:11865/146‑1 (MQ=60)
tgcCCGCGAATGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCG < NB501016:282:H2V7GAFX2:4:11410:15335:12828/146‑1 (MQ=60)
C‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCGGATC < NB501016:282:H2V7GAFX2:3:11404:23389:13639/151‑1 (MQ=60)
|
GACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCGGATC > NC_002947_CJ‑RC/1932523‑1932788
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
