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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,602,506 |
T→A |
D93E (GAT→GAA) |
yjjU → |
patatin family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,602,506 | 0 | T | A | 100.0%
| 111.5
/ NA
| 29 | D93E (GAT→GAA) | yjjU | patatin family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (17/12); total (17/12) |
CCTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGATCCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCCGTT > NZ_CP009273/4602425‑4602583
|
ccTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTgcg > 2:241248/1‑90 (MQ=255)
tctcGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCt > 1:570196/1‑90 (MQ=255)
gTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCg > 1:367525/1‑90 (MQ=255)
tttATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGt < 1:269818/90‑1 (MQ=255)
tttATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGt < 2:502461/90‑1 (MQ=255)
tGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTggagga < 1:122811/90‑1 (MQ=255)
tGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTggagga < 2:326260/90‑1 (MQ=255)
gCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGaa > 2:284959/1‑90 (MQ=255)
gCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTAt > 1:115822/1‑90 (MQ=255)
cGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGa > 2:227321/1‑90 (MQ=255)
aCGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCg > 2:200643/1‑90 (MQ=255)
gcgcgcAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGAc < 1:192663/90‑1 (MQ=255)
gcgcgcAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGAc > 1:598093/1‑90 (MQ=255)
gcAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGActggc > 2:438403/1‑90 (MQ=255)
cAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGActggct < 2:135299/90‑1 (MQ=255)
tcatGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAgg > 2:66526/1‑90 (MQ=255)
atGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGcc < 1:554740/90‑1 (MQ=255)
atGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGcc > 2:255323/1‑90 (MQ=255)
atGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGcc < 2:34647/90‑1 (MQ=255)
cTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGc < 1:126606/90‑1 (MQ=255)
ataCCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGActggct > 1:556881/1‑73 (MQ=255)
ataCCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGActggct < 2:556881/73‑1 (MQ=255)
acaAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAg > 2:202308/1‑90 (MQ=255)
aaaaCGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGAt < 1:445460/90‑1 (MQ=255)
aaaCGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGGGGAGGCCACTGCAAGCCAGATg > 1:407063/1‑90 (MQ=255)
aCGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGcc > 1:60572/1‑90 (MQ=255)
aCGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGGGTAGGCCCCTGCAAGCCAGATGcc > 1:394911/1‑90 (MQ=255)
aCGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGGGGAGGCCACTGCAAGCCAGATGcc > 1:280320/1‑90 (MQ=255)
cgAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCCGtt < 2:570196/90‑1 (MQ=255)
|
CCTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGATCCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCCGTT > NZ_CP009273/4602425‑4602583
|
| 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
GCGCAGAACCTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGATCCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCCGTTGCAAATGGATACCG > NZ_CP009273/4602417‑4602597
|
GCGCAGAACCTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCT > SRR3721989.582560/1‑100 (MQ=60)
ACCTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCG > SRR3721989.374705/1‑100 (MQ=60)
TTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATC < SRR3721989.274624/100‑1 (MQ=60)
TCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTAT > SRR3721989.117942/1‑100 (MQ=60)
TGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCG < SRR3721989.125061/100‑1 (MQ=60)
GCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGAC > SRR3721989.611092/1‑100 (MQ=60)
GCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGG < SRR3721989.196182/100‑1 (MQ=60)
ATCATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGgggccctgtctc > SRR3721989.568960/1‑88 (MQ=60)
ATGCGCTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCC < SRR3721989.566767/100‑1 (MQ=60)
CTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATG < SRR3721989.128931/100‑1 (MQ=60)
CTATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGGGGAGGCCACTGCAAGCCAGATG > SRR3721989.415398/1‑100 (MQ=60)
ATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCC > SRR3721989.61639/1‑100 (MQ=60)
ATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGGGTAGGCCCCTGCAAGCCAGATGCC > SRR3721989.402916/1‑100 (MQ=60)
ATACCACAAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGGGGAGGCCACTGCAAGCCAGATGCC > SRR3721989.285437/1‑100 (MQ=60)
AAAACGCGAATTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCCGTTGCAA < SRR3721989.454749/100‑1 (MQ=60)
TTTTTCGAACCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCctgtctcttatacacatctgacgctgccg > SRR3721989.40252/1‑71 (MQ=60)
|
GCGCAGAACCTCTCGGCGTTTATCTGCAATCAGCCCGGTTACGCGCGCAAAGTCATCATGCGCTATACCACAAAACGCGAATTTTTCGATCCATTGCGCTTTGTCCGTGGAGGAAATCTTATCGATCTCGACTGGCTGGTGGAGGCCACTGCAAGCCAGATGCCGTTGCAAATGGATACCG > NZ_CP009273/4602417‑4602597
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
