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 F1 I1 R1
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
159,381 |
+G |
intergenic (‑13/‑342) |
h16_B0138 ← / → h16_B0139 |
transcriptional regulator, IclR‑family/conserved hypothetical transmembrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 159,380 | 1 | . | G | 100.0%
| 57.6
/ NA
| 19 | intergenic (‑12/‑343) | h16_B0138/h16_B0139 | transcriptional regulator, IclR‑family/conserved hypothetical transmembrane protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (10/9); total (10/9) |
GCGCCAGCGCTTCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCC > AM260480/159251‑159501
|
gcgcCAGCGCTTCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑ggcg < 1:254211/134‑4 (MQ=255)
ccAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAA‑ggtcgc < 1:972004/133‑6 (MQ=255)
caccacCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGc < 2:965902/133‑1 (MQ=255)
accTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac < 1:119448/134‑1 (MQ=255)
cAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg < 1:233374/81‑1 (MQ=25)
cAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg > 2:233374/1‑81 (MQ=25)
cAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCa > 1:21135/1‑134 (MQ=255)
cGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGTGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGccc > 1:672956/1‑134 (MQ=25)
aCCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGtt > 1:749631/1‑111 (MQ=21)
aCCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGtt < 2:749631/111‑1 (MQ=21)
aCCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAgctgggctgg > 2:327753/1‑134 (MQ=255)
aGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg > 1:50890/1‑59 (MQ=18)
aGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg < 2:50890/59‑1 (MQ=18)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCgtgg > 1:300281/1‑71 (MQ=14)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCgtgg < 2:300281/71‑1 (MQ=14)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTgg > 2:866999/1‑134 (MQ=255)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTgg > 1:609945/1‑134 (MQ=255)
gCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTggg < 2:21135/134‑1 (MQ=255)
cACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGTGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAg < 2:672956/132‑1 (MQ=25)
aGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGcc > 1:756888/1‑134 (MQ=255)
|
GCGCCAGCGCTTCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCC > AM260480/159251‑159501
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGCGCCAGCGCTTCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC > AM260480/159250‑159517
|
CGCGCCAGCGCTTCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGC < GWNJ‑0478:712:GW2002102894th:2:1116:12268:92537/150‑1 (MQ=60)
aagacggcatacgagctgtagctccgtctcgtgggctcggagatgtgtataagagacagGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCAC < GWNJ‑0478:712:GW2002102894th:2:1114:1611:20186/91‑1 (MQ=60)
TCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCAC < GWNJ‑0478:712:GW2002102894th:2:2213:16493:56552/149‑1 (MQ=60)
gctccgtctcgtgggctcggagatgtgtataagagacagGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCAC < GWNJ‑0478:712:GW2002102894th:2:1114:11965:67517/111‑1 (MQ=60)
tttaggatactatttgtttcttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGT < GWNJ‑0478:712:GW2002102894th:2:1203:11983:75639/51‑1 (MQ=43)
CACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCC < GWNJ‑0478:712:GW2002102894th:2:1108:11962:100779/150‑1 (MQ=60)
GCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCAC > GWNJ‑0478:712:GW2002102894th:2:1103:18880:51288/1‑150 (MQ=60)
TCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGTGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCC > GWNJ‑0478:712:GW2002102894th:2:2110:18825:22293/1‑150 (MQ=60)
GCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCctgtctctt > GWNJ‑0478:712:GW2002102894th:2:2114:8552:63359/1‑141 (MQ=60)
AACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttct > GWNJ‑0478:712:GW2002102894th:2:1102:7776:52297/1‑89 (MQ=60)
ACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCtgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:1205:5749:17149/1‑102 (MQ=60)
ACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGG > GWNJ‑0478:712:GW2002102894th:2:2106:16520:31293/1‑150 (MQ=60)
AGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCG > GWNJ‑0478:712:GW2002102894th:2:2116:10294:6179/1‑150 (MQ=60)
GTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaagaaagaccctaata > GWNJ‑0478:712:GW2002102894th:2:2201:16379:31975/1‑54 (MQ=51)
CTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGT > GWNJ‑0478:712:GW2002102894th:2:2115:6226:68946/1‑150 (MQ=60)
GCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaacataaaactaa > GWNJ‑0478:712:GW2002102894th:2:2213:4011:50657/1‑61 (MQ=60)
AGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC < GWNJ‑0478:712:GW2002102894th:2:1215:11696:89068/150‑1 (MQ=60)
AGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC > GWNJ‑0478:712:GW2002102894th:2:1212:14607:84138/1‑150 (MQ=60)
|
CGCGCCAGCGCTTCCAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC > AM260480/159250‑159517
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
