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 |
|
A2 F24 I1 R1
|
60 |
68.7 |
2919236 |
98.6% |
2878366 |
146.9 |
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 | 96.0%
| 83.4
/ ‑3.4
| 25 | 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 . (1/0); new base C (21/3); total (22/3) |
| 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 |
AGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT > NC_002947_CJ‑RC/1932526‑1932781
|
aGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCCGGGAACACCCCGCCGACAAAAGATATGCCGGCCCCGGTAGGCCCGGCGTTG‑CCGCCAACGGCGGCAACACACCCCCCAAATGtggc > 6:123115/1‑146 (MQ=255)
cgGGCAAGCCCGCTCCTACAAAGGATATG‑CGTCCCCAGTAGGAGCGGGCTTGCCCGCGAACGGCTGCAAGGCAGCCCCAAATTGTAGACTAAGCGGATCAGCGATACGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTgg > 6:129513/1‑149 (MQ=255)
gCAAGCCCGCTCCTACAAAGTATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg < 8:115274/110‑1 (MQ=255)
gCAAGCCCGCTCCTACAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAgg > 7:115274/1‑110 (MQ=255)
gCCCGCTCCTACAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTc > 2:102402/1‑147 (MQ=255)
ccGCTCCTACAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGc > 7:61019/1‑149 (MQ=255)
ccGCTCCTACAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGc > 6:184959/1‑149 (MQ=255)
aCAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATg > 2:227394/1‑149 (MQ=255)
cAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATg > 5:196802/1‑148 (MQ=255)
aaaGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGca > 2:297521/1‑149 (MQ=255)
aaaGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAAATGTCGACTACGCGGATCAGCGATCCGGCAGGGAGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGca > 6:23784/1‑149 (MQ=255)
aGGATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGcaca > 3:119999/1‑149 (MQ=255)
gATATG‑CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCAcat > 4:351966/1‑148 (MQ=255)
gTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTg > 5:245689/1‑149 (MQ=255)
cccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGt > 7:201207/1‑117 (MQ=255)
cccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGt < 8:201207/117‑1 (MQ=255)
cccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGcc > 5:143545/1‑148 (MQ=255)
cccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGcc > 6:302004/1‑148 (MQ=255)
ccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGa > 4:147562/1‑149 (MQ=255)
ccTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACCCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGACCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGa > 7:320235/1‑149 (MQ=255)
cTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAt > 4:163201/1‑149 (MQ=255)
gTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGt > 1:191474/1‑149 (MQ=255)
tAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCa < 6:182105/85‑1 (MQ=255)
tAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCa > 5:182105/1‑85 (MQ=255)
gCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATAttt > 5:113493/1‑149 (MQ=255)
|
AGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATG‑CGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTT > NC_002947_CJ‑RC/1932526‑1932781
|
| 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‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCGGATCAC > NC_002947_CJ‑RC/1932523‑1932790
|
ccgactaccgtatcccacaacagaatctcccccgccgtggcgccgccgccgggccgccgtggccgcccccccccaacactctaccctacctcccccgccccgggccggcccccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCG < NB501016:282:H2V7GAFX2:1:11312:14309:13674/34‑1 (MQ=33)
aaaaccggggggccgttttggggcccgtggggggccaccccccaacaaaaaattttatgccgccccgtttggggggggggtgccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGT < NB501016:282:H2V7GAFX2:1:21110:20571:15537/67‑1 (MQ=60)
gggggggcggcgctttgcggcggtcgcgggccaagccggttttaacatttgtggtgcggcccttgtgggggggtggtggccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTC < NB501016:282:H2V7GAFX2:2:11211:23151:14004/69‑1 (MQ=60)
ggggcgccgtctgggcggcgggcgccggccccccccgatacaaattattgtgggccgcggtccgtcccgggggggcccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCT < NB501016:282:H2V7GAFX2:4:11406:11462:3061/73‑1 (MQ=60)
gggggggggggggggggggggggggtccgccgcccccatcaaatttttcggggcgcctgtggggggggggccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCC < NB501016:282:H2V7GAFX2:2:21307:4629:1214/75‑1 (MQ=60)
GGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGG > NB501016:282:H2V7GAFX2:4:11510:15476:10703/1‑112 (MQ=60)
cccgctcctacaggggacgcatatccttTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCT > NB501016:282:H2V7GAFX2:4:11403:17145:9994/29‑151 (MQ=60)
ccccacaaaaaaactttcccgcccccgttgtgggggggggcccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCT < NB501016:282:H2V7GAFX2:2:21311:17943:14465/106‑1 (MQ=60)
CCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCT > NB501016:282:H2V7GAFX2:4:11412:20571:6154/1‑151 (MQ=60)
aaaaaaatttattgggccgcgcggggggggggggccccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATA < NB501016:282:H2V7GAFX2:1:11208:3869:9159/111‑1 (MQ=60)
ACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGC > NB501016:282:H2V7GAFX2:3:21402:19822:19647/1‑150 (MQ=60)
AAGGATATGCGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACAT > NB501016:282:H2V7GAFX2:2:11212:22369:11632/1‑151 (MQ=60)
CGTCCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGC > NB501016:282:H2V7GAFX2:3:21501:16035:7748/1‑151 (MQ=60)
CCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCG > NB501016:282:H2V7GAFX2:3:11604:11844:16457/1‑150 (MQ=60)
CCCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTT > NB501016:282:H2V7GAFX2:4:21403:13134:8107/1‑119 (MQ=60)
CCCTGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACCCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGACCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGAT > NB501016:282:H2V7GAFX2:4:21601:14610:19445/1‑151 (MQ=60)
gctgtgtgggggggcccccCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATG < NB501016:282:H2V7GAFX2:1:11205:9982:2421/132‑1 (MQ=60)
TGTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTT > NB501016:282:H2V7GAFX2:1:21101:16637:14631/1‑151 (MQ=60)
GTAGGAGCGGGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAG > NB501016:282:H2V7GAFX2:3:11611:16125:17701/1‑87 (MQ=60)
GGCTTGCCCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTG > NB501016:282:H2V7GAFX2:3:11511:14960:7522/1‑151 (MQ=60)
CGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCGGATCAC < NB501016:282:H2V7GAFX2:3:21512:21855:13729/151‑1 (MQ=60)
|
GACAGCGGCATTGCAGGTCTCACGAAAATAGCAGTAAACGCTGGGGCCGCTTTGCGGCCCTTCGCGGGCAAGCCCGCTCCTACAAAGGATATGCGTCCCCTGTAGGAGCGGGCTTG‑CCGCGAAGGGCTGCAAGGCAGCCCCAAATTGTCGACTACGCGGATCAGCGATCCGGCAGGGTGATGTTCAGCTCCAGAATCGAGCAGCTGCCCTGGTTTTCCAGCTCGATATGCACATCATCGTTGCCGATGTTCACATATTTGCGGATCAC > NC_002947_CJ‑RC/1932523‑1932790
|
| 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: ‑ |
