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
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
547,879 |
2 bp→GA |
coding (595‑596/630 nt) |
h16_A0522 ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 547,879 | 0 | A | G | 100.0%
| 89.9
/ NA
| 24 | L199S (CTC→TCC) | h16_A0522 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/9); total (15/9) |
| * | AM260479 | 547,880 | 0 | G | A | 100.0%
| 89.2
/ NA
| 24 | L199S (CTC→TCC) | h16_A0522 | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (15/9); total (15/9) |
GTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGC > AM260479/547751‑547972
||
gTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGgacagc < 1:439824/134‑1 (MQ=255)
gTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGc > 1:600714/1‑134 (MQ=255)
agcagcGAGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTg < 2:850815/134‑1 (MQ=255)
gcagcGAGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGc < 2:600714/134‑1 (MQ=255)
gCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTgc > 1:285727/1‑134 (MQ=255)
aTGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGgc > 1:667845/1‑134 (MQ=255)
cGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCa < 1:358430/103‑1 (MQ=255)
cGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCa > 2:358430/1‑103 (MQ=255)
aaCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTg > 1:769314/1‑134 (MQ=255)
aaCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTg > 1:52489/1‑134 (MQ=255)
aCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTgcg > 1:744337/1‑116 (MQ=255)
aCAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTgcg < 2:744337/116‑1 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGc < 1:108401/64‑1 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGc > 2:108401/1‑64 (MQ=255)
gcgcgcg‑cCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGtt > 2:177932/1‑134 (MQ=255)
cgcgccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTg > 1:81225/5‑80 (MQ=255)
cgcgccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTg < 2:81225/76‑1 (MQ=255)
gcgccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGc < 1:459839/77‑1 (MQ=255)
gcgccGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGc > 2:459839/4‑80 (MQ=255)
cGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGa < 1:915893/71‑1 (MQ=255)
cGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGa > 2:915893/1‑71 (MQ=255)
cGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTgccgc > 1:394090/1‑134 (MQ=255)
cGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTgccgc > 1:318295/1‑134 (MQ=255)
ccACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCa > 1:666695/1‑45 (MQ=38)
ccACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCa < 2:666695/45‑1 (MQ=38)
||
GTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGC > AM260479/547751‑547972
|
| 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
GGTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTCGATGCGGCGCAGGC > AM260479/547750‑548017
|
GGTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTC < GWNJ‑0478:712:GW2002102894th:2:1213:8309:78733/150‑1 (MQ=60)
GCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCC > GWNJ‑0478:712:GW2002102894th:2:2107:15888:91595/1‑150 (MQ=60)
acggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagatcCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGA < GWNJ‑0478:712:GW2002102894th:2:1108:16127:24194/91‑1 (MQ=60)
acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGT < GWNJ‑0478:712:GW2002102894th:2:2211:10668:62866/101‑1 (MQ=60)
agctccgtctcgtgggctcggagatgtgtataagagacagAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCG < GWNJ‑0478:712:GW2002102894th:2:1212:6314:92202/110‑1 (MQ=60)
atgtgtataagagacaGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGC < GWNJ‑0478:712:GW2002102894th:2:1208:11871:2017/134‑1 (MQ=60)
AGTCGGTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCG > GWNJ‑0478:712:GW2002102894th:2:1202:7646:33224/1‑150 (MQ=60)
GTCATGGGTTGCGACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCC > GWNJ‑0478:712:GW2002102894th:2:2110:3130:12916/1‑150 (MQ=60)
ACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGG > GWNJ‑0478:712:GW2002102894th:2:2201:18236:22968/1‑150 (MQ=60)
ACATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGG > GWNJ‑0478:712:GW2002102894th:2:1102:11172:59763/1‑150 (MQ=60)
CATGAATCGTATCCAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCctgt > GWNJ‑0478:712:GW2002102894th:2:2114:3010:64792/1‑146 (MQ=60)
CAACAGGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCctgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:1107:6837:50405/1‑110 (MQ=60)
GGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCC > GWNJ‑0478:712:GW2002102894th:2:1204:12727:45318/1‑150 (MQ=60)
GGTTGTAGCGCGCG‑CCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCC > GWNJ‑0478:712:GW2002102894th:2:1211:2236:19577/1‑150 (MQ=60)
atctttcgccgcgCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttcttcttgaaaaacaaaaaacgtc > GWNJ‑0478:712:GW2002102894th:2:1215:3597:10394/14‑68 (MQ=60)
GCGAAAGATTAGGTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2110:4035:6180/1‑75 (MQ=60)
GTTCCACTCCGGACAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCaatgcgcctacacctgtctcttatacacatctccgagcccacgagacggagctacat > GWNJ‑0478:712:GW2002102894th:2:2104:6239:85160/1‑93 (MQ=60)
|
GGTGGCAGCTCTTCGGTGAACAGTTCGATCAGCAGCGAGTCGGTCATGGGTTGCGACATGAATCGTAT‑CAACAGGTTGTAGCGCGCGCCCGCTTGTCAGCAGCGCGGCGAAAGATTAGGTTCCACTCCGAGCAGCAGCCACAGGCCGTTCTGTTGCCGGAATTGCAGCGTGGTGTAGGCGCATTGCGCGGCCGCCGCGGCGCTGGCCGCGCCGTTGCTGCCGCCGCGGCTGCCTGCAGCCGGGAAGCGTGCGTCGATGCGGCGCAGGC > AM260479/547750‑548017
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
