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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,410,868 |
A→T |
G103G (GGA→GGT) |
yfcC → |
putative basic amino acid antiporter YfcC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,410,868 | 0 | A | T | 100.0%
| 194.9
/ NA
| 53 | G103G (GGA→GGT) | yfcC | putative basic amino acid antiporter YfcC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (28/25); total (28/25) |
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAC > NZ_CP009273/2410783‑2410951
|
cTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGa < 1:758008/90‑1 (MQ=255)
aGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAAt > 1:1029645/1‑90 (MQ=255)
tATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATAc < 2:61269/90‑1 (MQ=255)
tCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACgg > 2:726626/1‑90 (MQ=255)
tCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACgg > 2:899184/1‑90 (MQ=255)
aCCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGa > 1:896312/1‑90 (MQ=255)
aCCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGa > 1:394507/1‑90 (MQ=255)
ccGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAc < 2:394507/90‑1 (MQ=255)
gcgTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAg > 2:164193/1‑90 (MQ=255)
gcgTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAg > 2:708003/1‑90 (MQ=255)
gcgTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAg > 2:263103/1‑90 (MQ=255)
gTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGcc > 2:73331/1‑90 (MQ=255)
gTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGcc > 1:185154/1‑90 (MQ=255)
gTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGcc > 1:500450/1‑90 (MQ=255)
gCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTgg > 1:482149/1‑90 (MQ=255)
cTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGc < 2:345407/90‑1 (MQ=255)
tGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGca < 2:896817/90‑1 (MQ=255)
tGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGca < 2:896312/90‑1 (MQ=255)
gTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTc < 2:839995/66‑1 (MQ=255)
gTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTc > 1:839995/1‑66 (MQ=255)
acgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatc < 1:726626/90‑1 (MQ=255)
acgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatc < 2:793385/90‑1 (MQ=255)
acgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatc < 1:1234604/90‑1 (MQ=255)
acgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatc < 1:1152662/90‑1 (MQ=255)
cgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatca > 2:53391/1‑90 (MQ=255)
cgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatca > 1:771693/1‑90 (MQ=255)
cgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatca > 1:1224610/1‑90 (MQ=255)
cgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatca > 1:1146440/1‑90 (MQ=255)
cgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatca > 2:704399/1‑90 (MQ=255)
ggCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGttt > 1:52545/1‑90 (MQ=255)
tGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCt < 1:708003/90‑1 (MQ=255)
gCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGa > 1:814677/1‑90 (MQ=255)
gggCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTgg > 2:803746/1‑90 (MQ=255)
gggCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTgg > 1:193992/1‑90 (MQ=255)
gCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcat > 1:924166/1‑64 (MQ=255)
gCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcat < 2:924166/64‑1 (MQ=255)
ccTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTggcgg < 2:221114/90‑1 (MQ=255)
cTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTggcggc < 1:1027144/90‑1 (MQ=255)
cTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTggcggc < 1:1204750/90‑1 (MQ=255)
tgatgaACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGgcggcg < 1:736101/90‑1 (MQ=255)
aCTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTg > 2:473248/1‑90 (MQ=255)
tCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCa > 1:1023527/1‑90 (MQ=255)
tCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCa > 2:314129/1‑90 (MQ=255)
cccGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCAt < 1:255646/90‑1 (MQ=255)
ccGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCAtt > 1:443037/1‑90 (MQ=255)
cGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATtg < 1:375877/90‑1 (MQ=255)
ttGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGa < 1:946071/90‑1 (MQ=255)
aaGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGc < 2:1023527/90‑1 (MQ=255)
aaGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGc < 2:482149/90‑1 (MQ=255)
gATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTa < 2:1177537/90‑1 (MQ=255)
ttAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACa > 2:599079/1‑90 (MQ=255)
aCCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGa < 1:523108/90‑1 (MQ=255)
cTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAc < 2:761967/90‑1 (MQ=255)
|
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAC > NZ_CP009273/2410783‑2410951
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGAAGCAGGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATA > NZ_CP009273/2410769‑2410959
|
tcagatgtgtataagagacagTCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGT < SRR3722089.477670/79‑1 (MQ=60)
GAAGCAGGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTT < SRR3722089.933858/100‑1 (MQ=60)
GGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAAT > SRR3722089.1045027/1‑100 (MQ=60)
CCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGA > SRR3722089.399314/1‑100 (MQ=60)
CCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGA > SRR3722089.909288/1‑100 (MQ=60)
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAC < SRR3722089.768120/100‑1 (MQ=60)
GTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCC > SRR3722089.506365/1‑100 (MQ=60)
GTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCC > SRR3722089.187467/1‑100 (MQ=60)
ACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGG > SRR3722089.487875/1‑100 (MQ=60)
GCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGctgtctcttataca > SRR3722089.851898/1‑86 (MQ=60)
CAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCA > SRR3722089.1243218/1‑100 (MQ=60)
CAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCA > SRR3722089.1163895/1‑100 (MQ=60)
CAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCA > SRR3722089.782130/1‑100 (MQ=60)
GTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTT > SRR3722089.53195/1‑100 (MQ=60)
ACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGC < SRR3722089.1253372/100‑1 (MQ=60)
ACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGC < SRR3722089.1170206/100‑1 (MQ=60)
ACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGC < SRR3722089.736078/100‑1 (MQ=60)
GGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGA > SRR3722089.826075/1‑100 (MQ=60)
ATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGG > SRR3722089.196432/1‑100 (MQ=60)
TGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGC < SRR3722089.717225/100‑1 (MQ=60)
GAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTctgtctcttatacaca > SRR3722089.937643/1‑84 (MQ=60)
CTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCA < SRR3722089.1042471/100‑1 (MQ=60)
CTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCA < SRR3722089.1223064/100‑1 (MQ=60)
CTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCA > SRR3722089.1038794/1‑100 (MQ=60)
TGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCAT < SRR3722089.745719/100‑1 (MQ=60)
GATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATT > SRR3722089.448353/1‑100 (MQ=60)
CCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGT < SRR3722089.258924/100‑1 (MQ=60)
CGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTAC < SRR3722089.380476/100‑1 (MQ=60)
TTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGG < SRR3722089.959950/100‑1 (MQ=60)
ACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATA < SRR3722089.529224/100‑1 (MQ=60)
|
CGAAGCAGGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATA > NZ_CP009273/2410769‑2410959
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
