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 |
1,807,028 |
T→C |
E121G (GAA→GGA) |
BW25113_RS09050 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,807,028 | 0 | T | C | 100.0%
| 99.4
/ NA
| 31 | E121G (GAA→GGA) | BW25113_RS09050 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (18/13); total (18/13) |
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTA > NZ_CP009273/1806947‑1807114
|
atataATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa < 2:568418/90‑1 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 1:1221540/90‑1 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 2:310668/90‑1 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 1:324216/90‑1 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 1:364636/90‑1 (MQ=255)
ttGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 2:1113398/90‑1 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa > 2:664097/1‑74 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 1:664097/74‑1 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCa > 2:268061/1‑90 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCa > 2:1434426/1‑90 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCa > 2:1362207/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 2:919295/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:1437527/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:925229/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCACTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:1173124/1‑90 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTc > 1:523458/1‑83 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTc < 2:523458/83‑1 (MQ=255)
tAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCt < 1:1513732/90‑1 (MQ=255)
gTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCttt > 2:723007/1‑90 (MQ=255)
gTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCttt > 1:1553626/1‑90 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACct > 2:629318/1‑90 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACct > 1:1547710/1‑90 (MQ=255)
accTGTTTTTTATAATGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACctc < 1:908097/90‑1 (MQ=255)
tttATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGa < 1:543936/90‑1 (MQ=255)
tGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCAc < 1:1434426/90‑1 (MQ=255)
gATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACt > 2:57046/1‑90 (MQ=255)
gATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACt > 2:1339250/1‑90 (MQ=255)
gATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACt > 2:959424/1‑90 (MQ=255)
aaTTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCAt > 1:177603/1‑90 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCAc < 2:1146413/79‑1 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCAc > 1:1146413/1‑79 (MQ=255)
tttcCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGattatta < 1:1362207/90‑1 (MQ=255)
|
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTA > NZ_CP009273/1806947‑1807114
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAATTATTACTC > NZ_CP009273/1806955‑1807124
|
agacagATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCC < SRR3722078.671701/94‑1 (MQ=60)
TTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCC < SRR3722078.1240760/100‑1 (MQ=60)
TTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCC < SRR3722078.369086/100‑1 (MQ=60)
TTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCC < SRR3722078.328192/100‑1 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722078.937925/1‑100 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722078.1460923/1‑100 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCACTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722078.1191391/1‑100 (MQ=60)
ATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAA > SRR3722078.529648/1‑100 (MQ=60)
TCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTT > SRR3722078.1578925/1‑100 (MQ=60)
TAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATAC < SRR3722078.1538420/100‑1 (MQ=60)
GTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCT > SRR3722078.1572921/1‑100 (MQ=60)
ACCTGTTTTTTATAATGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAAT < SRR3722078.920333/100‑1 (MQ=60)
TTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTAC < SRR3722078.550358/100‑1 (MQ=60)
ATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCAT > SRR3722078.179682/1‑100 (MQ=60)
TGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAG < SRR3722078.1457766/100‑1 (MQ=60)
GATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGC > SRR3722078.1164064/1‑100 (MQ=60)
TTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAATTATTACTC < SRR3722078.1384104/100‑1 (MQ=60)
|
TTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAATTATTACTC > NZ_CP009273/1806955‑1807124
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
