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 F2 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,153,816 |
T→C |
S84P (TCA→CCA) |
btuB → |
TonB‑dependent vitamin B12 receptor BtuB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,153,816 | 0 | T | C | 94.1%
| 141.3
/ 0.9
| 51 | S84P (TCA→CCA) | btuB | TonB‑dependent vitamin B12 receptor BtuB |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (24/24); total (25/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01 |
CGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > NZ_CP009273/4153732‑4153901
|
cGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCCGCTCCCctct > 2:1043606/1‑90 (MQ=255)
gCTGGCAGTCGACCTCGGTCAGTGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGGTCAGGTCAGCTCCCATCTa > 2:459692/1‑90 (MQ=255)
gACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTTAGGGGAGCTCCCCTCtttttttttttt > 1:1345373/1‑88 (MQ=255)
aCCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTcgc < 1:1043606/90‑1 (MQ=255)
cGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTa < 2:1258275/90‑1 (MQ=255)
gTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCCCCCATCTATTTTTTTTTGCGGTACa > 1:546115/1‑90 (MQ=255)
tCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACaa < 2:1280088/90‑1 (MQ=255)
gatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 1:129909/90‑1 (MQ=255)
gatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 2:1220961/90‑1 (MQ=255)
gatgTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 2:408671/90‑1 (MQ=255)
tgtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAg < 2:206052/90‑1 (MQ=255)
gtgCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGt < 2:308311/90‑1 (MQ=255)
gctgcGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCa < 2:352371/90‑1 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGGACAAAAGCCCGTCAtgt > 1:60713/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTTGCGGGACAAAAGCCAGTCAtgt > 2:959821/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCAtgt > 2:798591/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCAGTCAtgt > 1:647660/1‑90 (MQ=255)
gcgcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCAtgt > 2:669788/1‑90 (MQ=255)
gcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATgtgt > 2:1387828/1‑90 (MQ=255)
gcCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATgtgt < 1:111544/90‑1 (MQ=255)
cGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTg < 2:342146/90‑1 (MQ=255)
cGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTg < 1:447589/90‑1 (MQ=255)
cGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTg < 2:1319846/90‑1 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCCTCTATTTTTTTTCGCGGGACAAATGCCAGTCATGGGTTgg > 2:1031728/1‑90 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTTTTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTgg > 1:266251/1‑90 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGGCATGTGTTgg > 2:334953/1‑90 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGtttg > 1:332884/1‑88 (MQ=255)
gTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTgg > 2:851504/1‑90 (MQ=255)
ggCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAAtt < 2:1345373/90‑1 (MQ=255)
cGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCCGTCATGTGTTGGTGTTAATTGa > 1:129884/1‑90 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 1:1387828/90‑1 (MQ=255)
gTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGAt < 2:1312979/90‑1 (MQ=255)
tCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTTTCGGTACAAAAGCCAGTCATGTGTTGGGGGTTATTGATg > 2:889807/1‑90 (MQ=255)
tatCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGt < 1:1531615/90‑1 (MQ=255)
tatCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGt < 2:1242290/90‑1 (MQ=255)
aCCCAAAACGGCGGGTCAGGTCAGCTCCCCTCTCTTTTTTTTCGCGGGACCAAAGCCCGCCAATGGTTGGGGGTAATTTATGGCGTACGc > 1:887884/1‑90 (MQ=255)
cAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTTGCGGGACAAATGCCAGTCATGTGTTGGGGTTAATTGATGGCGGACGCCTg > 1:280288/1‑90 (MQ=255)
aaaaCGGCGGTTCAGGGCAGCTCTCATCTATTTTTATTTGCGGTAAAAAAGGCAGTCATGGGGTGGGGTTAATTTATGGCGTACGCCTGa > 1:1226108/1‑90 (MQ=255)
aaaCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGGGTTAATTGATGGCGTACGCCTGaa > 2:826654/1‑90 (MQ=255)
aaCGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAt < 2:1226108/90‑1 (MQ=255)
aaCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAt < 1:135135/90‑1 (MQ=255)
aaCGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAt < 1:915004/90‑1 (MQ=255)
ggcggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTg > 2:157890/1‑90 (MQ=255)
gcggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc > 1:1420622/1‑47 (MQ=255)
gcggTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGcc < 2:1420622/47‑1 (MQ=255)
gTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGa < 1:583261/90‑1 (MQ=255)
cAGCTCCCATCTATTTTTATTCTCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGt < 2:388860/90‑1 (MQ=255)
cAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGt < 2:129884/90‑1 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTgg < 1:20929/90‑1 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTgg > 2:1581508/1‑90 (MQ=255)
gCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTgg > 1:320836/1‑90 (MQ=255)
|
CGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > NZ_CP009273/4153732‑4153901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCGAC > NZ_CP009273/4153721‑4153911
|
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATC < SRR3722078.872347/100‑1 (MQ=60)
GTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCCCCCATCTATTTTTTTTTGCGGTACA > SRR3722078.552559/1‑100 (MQ=60)
ACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATG < SRR3722078.1059188/100‑1 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTCGCGGGACAAAAGCCCGTCATGT > SRR3722078.61425/1‑100 (MQ=60)
ATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGT > SRR3722078.655104/1‑100 (MQ=60)
GATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGT < SRR3722078.131408/100‑1 (MQ=60)
GTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTTTTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTGG > SRR3722078.269507/1‑100 (MQ=60)
GTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCCTCTATTTTTTTTTGCGGGACAAAAGCCAGTCATGTGTTTG > SRR3722078.336954/1‑100 (MQ=60)
GCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAAT < SRR3722078.112863/100‑1 (MQ=60)
CGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTG < SRR3722078.452946/100‑1 (MQ=60)
GTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTTTTTGCGGGACAAAAGCCCGTCATGTGTTGGTGTTAATTGA > SRR3722078.131383/1‑100 (MQ=60)
taagagacagCCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCC < SRR3722078.962852/90‑1 (MQ=60)
GTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCC < SRR3722078.1410246/100‑1 (MQ=60)
CGATATCACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTTGCGGGACAAATGCCAGTCATGTGTTGGGGTTAATTGATGGCGGACGCCTG > SRR3722078.283709/1‑100 (MQ=60)
GATATCACCCAAAACGGCGGTTCAGGGCAGCTCTCATCTATTTTTATTTGCGGTAAAAAAGGCAGTCATGGGGTGGGGTTAATTTATGGCGTACGCCTGA > SRR3722078.1245421/1‑100 (MQ=60)
TATCACCCAAAACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAAT < SRR3722078.1556576/100‑1 (MQ=60)
ACCCAAAACGGCGGTTCAGGGCAGCTCCCATCTATTTTTATTTGCGGTACAAATGCCAGTCATGTGTctgtctcttatacacatctgacgctgccgacga > SRR3722078.1443691/1‑67 (MQ=60)
AACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGG < SRR3722078.136697/100‑1 (MQ=60)
AACGGCGGTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGG < SRR3722078.927422/100‑1 (MQ=60)
GTTCAGGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGG > SRR3722078.324762/1‑100 (MQ=60)
GGTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTG > SRR3722078.934864/1‑100 (MQ=60)
GTCAGCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGC < SRR3722078.590057/100‑1 (MQ=60)
GCTCCCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCGAC < SRR3722078.21193/100‑1 (MQ=60)
|
AGGATATCGACCGCTGGCAGTCGACCTCGGTCAATGATGTGCTGCGCCGTCTTCCGGGCGTCGATATCACCCAAAACGGCGGTTCAGGTCAGCTCTCATCTATTTTTATTCGCGGTACAAATGCCAGTCATGTGTTGGTGTTAATTGATGGCGTACGCCTGAATCTGGCGGGGGTGAGTGGTTCTGCCGAC > NZ_CP009273/4153721‑4153911
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
