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 |
1,844,118 |
A→G |
E342G (GAA→GGA) |
sppA → |
signal peptide peptidase SppA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,844,118 | 0 | A | G | 100.0%
| 97.6
/ NA
| 29 | E342G (GAA→GGA) | sppA | signal peptide peptidase SppA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/14); total (15/14) |
TTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCT > NZ_CP009273/1844032‑1844202
|
ttacgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAAc > 2:859667/1‑90 (MQ=255)
acgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTc < 2:947509/90‑1 (MQ=255)
ttacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAggg > 2:643149/1‑90 (MQ=255)
ttacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAggg > 2:1176010/1‑90 (MQ=255)
aaaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCg < 2:1128069/90‑1 (MQ=255)
ccGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGAt < 1:608175/90‑1 (MQ=255)
gCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATAcc < 1:1176010/90‑1 (MQ=255)
gCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATAcc < 2:674269/90‑1 (MQ=255)
gCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATAcc < 1:643149/90‑1 (MQ=255)
gTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGcac > 2:162878/1‑90 (MQ=255)
cAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAAt > 2:986491/1‑90 (MQ=255)
aGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATc > 1:1149641/1‑90 (MQ=255)
cATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTTCGGCACAAATCcg > 1:338997/1‑90 (MQ=255)
gtcgtcTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCt < 2:1193058/90‑1 (MQ=255)
gtcTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGc > 2:471397/1‑90 (MQ=255)
ggCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCg > 2:712632/1‑43 (MQ=255)
ggCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCg < 1:712632/43‑1 (MQ=255)
ggCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTg > 2:12742/1‑46 (MQ=255)
ggCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTg < 1:12742/46‑1 (MQ=255)
atggCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTg < 2:1028667/90‑1 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 1:1016351/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 1:1068360/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 1:230875/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:1156521/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:103472/1‑90 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 2:716902/90‑1 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 2:856161/90‑1 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 1:905156/90‑1 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 2:1068360/90‑1 (MQ=255)
|
TTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCT > NZ_CP009273/1844032‑1844202
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GCGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC > NZ_CP009273/1844019‑1844216
|
GCGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGG < SRR3722089.304710/100‑1 (MQ=60)
GCGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGG < SRR3722089.428175/100‑1 (MQ=60)
TTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGG < SRR3722089.3227/100‑1 (MQ=60)
caccgagatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATAC < SRR3722089.838204/44‑1 (MQ=60)
ccaccgagatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagTGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCAC < SRR3722089.917421/43‑1 (MQ=60)
atggtcgtcggcagcgtcagatgtgtataagagacagCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCAC < SRR3722089.721906/63‑1 (MQ=60)
gtcgtcggcagcgtcagatgtgtataagagacagCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGC < SRR3722089.12895/66‑1 (MQ=60)
CCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGG < SRR3722089.615730/100‑1 (MQ=60)
GCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCAC < SRR3722089.1193932/100‑1 (MQ=60)
GCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCAC < SRR3722089.651368/100‑1 (MQ=60)
TACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATC > SRR3722089.1167143/1‑100 (MQ=60)
CCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTTCGGCACAAATCCG > SRR3722089.343222/1‑100 (MQ=60)
ATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCC > SRR3722089.1084399/1‑100 (MQ=60)
ATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCC > SRR3722089.233804/1‑100 (MQ=60)
ATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCC > SRR3722089.1031495/1‑100 (MQ=60)
ATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGC > SRR3722089.61238/1‑100 (MQ=60)
CGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT < SRR3722089.918303/100‑1 (MQ=60)
AGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAG < SRR3722089.886618/100‑1 (MQ=60)
GGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC < SRR3722089.641848/100‑1 (MQ=60)
GGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC < SRR3722089.1097536/100‑1 (MQ=60)
GGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC < SRR3722089.84910/100‑1 (MQ=60)
|
GCGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC > NZ_CP009273/1844019‑1844216
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
