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 |
1,844,118 |
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%
| 142.3
/ NA
| 43 | E342G (GAA→GGA) | sppA | signal peptide peptidase SppA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (23/20); total (23/20) |
TTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCT > NZ_CP009273/1844032‑1844202
|
ttacgattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAAc > 2:653337/1‑90 (MQ=255)
gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAg > 2:1428346/1‑90 (MQ=255)
gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAg > 2:1299578/1‑90 (MQ=255)
gattacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAg > 2:1280793/1‑90 (MQ=255)
ttacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAggg > 2:893322/1‑90 (MQ=255)
ttacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAggg > 1:545587/1‑90 (MQ=255)
ttacgCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCCAATGGCGCAATTATGGATGGCGAGGGAACTCAggg > 1:389847/1‑90 (MQ=255)
aaaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCg < 2:1479689/90‑1 (MQ=255)
aaCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCgg < 1:240796/90‑1 (MQ=255)
aCGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGt > 2:609732/1‑90 (MQ=255)
gCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGa > 1:35005/1‑90 (MQ=255)
ccGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGAt < 1:1276393/90‑1 (MQ=255)
gCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATAcc < 2:555497/90‑1 (MQ=255)
gCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATAcc < 1:162597/90‑1 (MQ=255)
tACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTgg > 1:744534/1‑75 (MQ=255)
tACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTgg < 2:744534/75‑1 (MQ=255)
ggTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGca > 2:381354/1‑90 (MQ=255)
gTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGcac < 2:750021/90‑1 (MQ=255)
ggTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGAc > 2:1239578/1‑90 (MQ=255)
tcgtcTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTc < 2:672968/90‑1 (MQ=255)
cTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCt > 2:1278096/1‑90 (MQ=255)
tttGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCtt < 1:318583/90‑1 (MQ=255)
ttGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTg > 2:375879/1‑90 (MQ=255)
aTGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGa > 2:759262/1‑90 (MQ=255)
tGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGaa < 1:488613/90‑1 (MQ=255)
tGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGaa < 1:275229/90‑1 (MQ=255)
aTTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGaaa < 2:1410626/90‑1 (MQ=255)
tggatggCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGa < 2:389847/90‑1 (MQ=255)
tggatggCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGa < 1:381354/90‑1 (MQ=255)
ggatggCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGAt < 1:739778/90‑1 (MQ=255)
gatggCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGAtt < 2:104522/90‑1 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:424536/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:981119/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:1548032/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:1522201/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:1408460/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 2:112426/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 1:57143/1‑90 (MQ=255)
gCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTcc > 1:1214994/1‑90 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCTCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 2:142855/90‑1 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 2:35005/90‑1 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 1:424536/90‑1 (MQ=255)
cGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCt < 1:100686/90‑1 (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
CGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCCC > NZ_CP009273/1844020‑1844217
|
CGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGA > SRR3722078.464180/1‑100 (MQ=60)
GTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGG > SRR3722078.552027/1‑100 (MQ=60)
GTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCCAATGGCGCAATTATGGATGGCGAGGGAACTCAGGG > SRR3722078.394588/1‑100 (MQ=60)
CATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGA > SRR3722078.35434/1‑100 (MQ=60)
AACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACT < SRR3722078.243734/100‑1 (MQ=60)
CGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCctgtc > SRR3722078.753970/1‑95 (MQ=60)
CCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGG < SRR3722078.1296681/100‑1 (MQ=60)
GCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCAC < SRR3722078.164490/100‑1 (MQ=60)
TTTGCTAATGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAG < SRR3722078.322487/100‑1 (MQ=60)
TGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCG < SRR3722078.494417/100‑1 (MQ=60)
TGGCGCAATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCG < SRR3722078.278584/100‑1 (MQ=60)
ATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCC > SRR3722078.57816/1‑100 (MQ=60)
ATTATGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCC > SRR3722078.1234095/1‑100 (MQ=60)
TGGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCG < SRR3722078.386009/100‑1 (MQ=60)
GGATGGCGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGT < SRR3722078.749122/100‑1 (MQ=60)
CGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT < SRR3722078.429651/100‑1 (MQ=60)
CGAGGGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAAT < SRR3722078.101877/100‑1 (MQ=60)
GGAACTCAGGGGAATGTTGGCGGTGATCCCCCTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC < SRR3722078.1129701/100‑1 (MQ=60)
GGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC < SRR3722078.1451570/100‑1 (MQ=60)
GGAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCC < SRR3722078.1316179/100‑1 (MQ=60)
GAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCCC < SRR3722078.826502/100‑1 (MQ=60)
|
CGCCATCAGTTATTACGATTACGCATTGAAAACGCCGGCAGATACCGGTGACAGCATCGGTGTCGTCTTTGCTAATGGCGCAATTATGGATGGCGAGGAAACTCAGGGGAATGTTGGCGGTGATACCACTGCGGCACAAATCCGCGACGCTCGCCTTGACCCGAAAGTGAAAGCGATTGTCCTGCGTGTTAATAGCCC > NZ_CP009273/1844020‑1844217
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
