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 |
AM260479 |
3,615,716 |
+C |
intergenic (+42/‑147) |
prfA → / → h16_A3341 |
protein chain release factor A (RF‑1)/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,615,715 | 1 | . | C | 100.0%
| 86.9
/ NA
| 23 | intergenic (+41/‑148) | prfA/h16_A3341 | protein chain release factor A (RF‑1)/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (13/10); total (13/10) |
ATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTA > AM260479/3615588‑3615830
|
aTGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAaca‑ccgcg < 2:417772/133‑5 (MQ=255)
aCGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGT‑aaag < 1:593782/134‑3 (MQ=255)
gCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGT‑aaagtcg > 1:405435/1‑129 (MQ=255)
aTGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGa > 2:749963/1‑133 (MQ=255)
tgTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAaca‑ccg < 1:250921/106‑3 (MQ=255)
tgTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAaca‑ccg > 2:250921/1‑104 (MQ=255)
gCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGt > 1:690719/1‑133 (MQ=255)
cTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCtt < 1:749963/134‑1 (MQ=255)
gAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAAc < 2:872428/134‑1 (MQ=255)
ggCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTgg > 1:48627/1‑134 (MQ=255)
gCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAaca‑ccg < 2:374290/72‑3 (MQ=255)
gCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAaca‑ccg > 1:374290/1‑70 (MQ=255)
tgctgcACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAg > 2:313475/1‑132 (MQ=255)
tgctgcACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAg < 1:176655/132‑1 (MQ=255)
tgctgcACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAg < 1:313475/132‑1 (MQ=255)
tgctgcACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAg > 2:176655/1‑132 (MQ=255)
ctgcACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAggcgg > 1:556317/1‑134 (MQ=255)
tgcACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAggcggc > 1:617093/1‑134 (MQ=255)
cGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATaa > 1:618231/1‑134 (MQ=255)
gTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGAtt < 2:405435/134‑1 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTaaa > 1:467831/1‑71 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTaaa < 2:467831/71‑1 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCtt > 2:183669/1‑76 (MQ=255)
aaaTGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCtt < 1:183669/76‑1 (MQ=255)
cAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGc > 2:748190/1‑134 (MQ=255)
gCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTa < 2:617093/134‑1 (MQ=255)
cGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTa > 1:593519/1‑123 (MQ=255)
cGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTa < 2:593519/123‑1 (MQ=255)
|
ATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTA > AM260479/3615588‑3615830
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ 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
TGTACAAGATCGACATGATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCG > AM260479/3615568‑3615840
|
acaacgtgttcgatgctgttttctttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑C < GWNJ‑0478:712:GW2002102894th:2:2106:3747:93337/49‑1 (MQ=60)
ATCGACATGATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑Ccgcgtaaag < GWNJ‑0478:712:GW2002102894th:2:2209:6917:75450/150‑10 (MQ=60)
ACATGATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGC > GWNJ‑0478:712:GW2002102894th:2:1211:9323:72623/1‑150 (MQ=60)
gtataagagacaGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGAT < GWNJ‑0478:712:GW2002102894th:2:1116:3477:70173/137‑1 (MQ=60)
ATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑Ccgcgtaaagtctgtctct > GWNJ‑0478:712:GW2002102894th:2:1204:3371:78637/1‑132 (MQ=60)
cgctgcttttatttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGAT < GWNJ‑0478:712:GW2002102894th:2:1105:2594:80699/56‑1 (MQ=55)
GACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTG < GWNJ‑0478:712:GW2002102894th:2:2107:19720:29182/150‑1 (MQ=60)
GATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTA > GWNJ‑0478:712:GW2002102894th:2:2113:20904:27183/1‑149 (MQ=60)
GGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGT > GWNJ‑0478:712:GW2002102894th:2:1102:8158:37176/1‑150 (MQ=60)
atgtagctccgtctcgtgggctcggagatgtgtataagagacagGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTA < GWNJ‑0478:712:GW2002102894th:2:1113:13524:83334/106‑1 (MQ=60)
GCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTA < GWNJ‑0478:712:GW2002102894th:2:2114:13315:65209/150‑1 (MQ=60)
ACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATctgtctcttatacacatctccgagcccacgagacggagctacatctcg > GWNJ‑0478:712:GW2002102894th:2:1208:16895:89162/1‑102 (MQ=60)
AGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGC > GWNJ‑0478:712:GW2002102894th:2:2102:16725:71106/1‑150 (MQ=60)
GGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCT > GWNJ‑0478:712:GW2002102894th:2:2106:10124:81215/1‑150 (MQ=60)
GCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAAT < GWNJ‑0478:712:GW2002102894th:2:1205:15309:101017/150‑1 (MQ=60)
GCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAAT < GWNJ‑0478:712:GW2002102894th:2:1113:5296:42157/150‑1 (MQ=60)
GCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAAT > GWNJ‑0478:712:GW2002102894th:2:2106:4590:88665/1‑150 (MQ=60)
GTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACctgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:1215:13623:23213/1‑101 (MQ=60)
ACCGGCCTTCCGCCCCGAACACCGCGTAAAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCG > GWNJ‑0478:712:GW2002102894th:2:2107:5447:27520/1‑148 (MQ=60)
|
TGTACAAGATCGACATGATCATGGACGGCGACATGGATGAGCTGCTGTCGGCACTGGCTTCGGAACACCAGGCTGATCAGCTTGCTGCACTTGGCGAAGAGTCGTAAGCACCACAAAATGTCGTGCAACCGGCCTTCCGCCCCGAACA‑CGCGT‑AAGTCGCCGATATCTTTGTATTTCTTGTAAATGCTTGAAACAGCACTGGTAGGGGTAAGGCGGCTGTCTATAATCGATTTCGACCGGCAAACGGAGAATGGTGCCGGGTAGTCACTCCCG > AM260479/3615568‑3615840
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
