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
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,529,526 |
+G |
intergenic (‑40/‑264) |
secA ← / → h16_A3265 |
preprotein translocase subunit SecA/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,529,524 | 1 | . | G | 100.0%
| 53.9
/ NA
| 15 | intergenic (‑38/‑266) | secA/h16_A3265 | preprotein translocase subunit SecA/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (7/8); total (7/8) |
ATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGG > AM260479/3529400‑3529636
|
aTTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCgg > 2:499536/1‑134 (MQ=255)
gcCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCcgg < 1:499536/134‑1 (MQ=255)
gcgATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGcc < 1:449226/128‑1 (MQ=255)
gcgATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGcc > 2:449226/1‑128 (MQ=255)
cAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTg > 2:5719/1‑134 (MQ=255)
cTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTTCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCaa < 1:123200/134‑1 (MQ=255)
aTTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCaaaa < 1:884985/133‑1 (MQ=255)
gagaAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGt > 2:905994/1‑134 (MQ=255)
gATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTg < 1:5719/134‑1 (MQ=255)
tCACCTGCGCGGAACCGGGCGGCACCACAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGt < 2:39393/133‑1 (MQ=255)
cTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCTGGGCGAGGAATGGATAGATTGGCGCAAAAc < 1:749373/79‑1 (MQ=255)
cTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCTGGGCGAGGAATGGATAGATTGGCGCAAAAc > 2:749373/1‑79 (MQ=255)
gAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCg < 1:874964/47‑1 (MQ=38)
gAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCg > 2:874964/1‑47 (MQ=38)
gAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAggg > 1:95567/1‑132 (MQ=255)
|
ATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGG > AM260479/3529400‑3529636
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ 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
CTCGAACTTCGGCTCCAGCGCATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGT > AM260479/3529379‑3529667
|
acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGga < GWNJ‑0478:712:GW2002102894th:2:1115:10309:47900/101‑3 (MQ=60)
GCATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGgactgtctcttatacacatct > GWNJ‑0478:712:GW2002102894th:2:2213:18089:90657/1‑129 (MQ=60)
CATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGgactgtctcttatacacatctc > GWNJ‑0478:712:GW2002102894th:2:1209:10831:48181/1‑128 (MQ=60)
CGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAA < GWNJ‑0478:712:GW2002102894th:2:1214:20384:66484/150‑1 (MQ=60)
CCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGAT < GWNJ‑0478:712:GW2002102894th:2:1213:3492:99167/150‑1 (MQ=60)
tttattattatttttatctttttctttattttgtttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaggGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGAT < GWNJ‑0478:712:GW2002102894th:2:1113:12173:11724/38‑1 (MQ=60)
tccctggatcattctctccttttctcctttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagccccagGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGAT < GWNJ‑0478:712:GW2002102894th:2:1107:18591:92595/38‑1 (MQ=60)
ttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATT < GWNJ‑0478:712:GW2002102894th:2:2206:4843:50059/77‑1 (MQ=60)
GCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTTCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATC < GWNJ‑0478:712:GW2002102894th:2:1109:3417:25569/150‑1 (MQ=60)
CATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCAT < GWNJ‑0478:712:GW2002102894th:2:2207:19040:13615/149‑1 (MQ=60)
agctccgtctcgtgggctcggagatgtgtataagagacagATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCTGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATG < GWNJ‑0478:712:GW2002102894th:2:2114:16830:35389/109‑1 (MQ=60)
CGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAG < GWNJ‑0478:712:GW2002102894th:2:1101:10994:43657/150‑1 (MQ=60)
GCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGC > GWNJ‑0478:712:GW2002102894th:2:1106:9514:51468/1‑148 (MQ=60)
GCTTTCACCTGCGCGGAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCG > GWNJ‑0478:712:GW2002102894th:2:1213:9347:33299/1‑58 (MQ=60)
GAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCtgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:1101:4165:45667/1‑119 (MQ=60)
GAACCGGGCGGCACCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGAT > GWNJ‑0478:712:GW2002102894th:2:2212:8930:46179/1‑150 (MQ=60)
CCCCAGGGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGGCCGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGT > GWNJ‑0478:712:GW2002102894th:2:1212:14773:32735/1‑150 (MQ=60)
|
CTCGAACTTCGGCTCCAGCGCATTGATCTGCGCCACCGTGCGGCGATATTGTTTGATCAGCCGCTCATTGCGGCTGCCGAAGACTTTCTTGAGAAGGCCGGTGATCATCGATTGCTTTCACCTGCGCGGAACCGGGCGGCACCCCA‑GGATGCGGGCTGCTCCGGCGGCCGGGCGAGGAATGGATAGATTGGCGCAAAACGCCGAGTTTATCATGTGCCGGGGTCACGG‑CGGAACGCGCCTGGCCCCGTCCCGCAAGGGCAGGCAAGCCTGCCGGATGTCGGCCACGCGT > AM260479/3529379‑3529667
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
