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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,814,267 |
A→G |
A368A (GCT→GCC) |
alaS ← |
alanine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,814,267 | 0 | A | G | 90.3%
| 77.3
/ 2.2
| 31 | A368A (GCT→GCC) | alaS | alanine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base A (2/1); new base G (11/17); total (13/18) |
| Fisher's exact test for biased strand distribution p-value = 5.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
CGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACG > NZ_CP009273/2814181‑2814351
|
cGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCa > 1:468191/1‑90 (MQ=255)
aaGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACt < 2:471091/90‑1 (MQ=255)
gTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctct < 1:570251/90‑1 (MQ=255)
tCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCtcttct > 2:678592/1‑90 (MQ=255)
aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCGGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc < 2:17301/90‑1 (MQ=255)
aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc < 1:779518/90‑1 (MQ=255)
aTCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTtcttcagt > 1:234298/1‑90 (MQ=255)
aTCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTtcttcagt > 1:763101/1‑90 (MQ=255)
tATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCa > 1:242577/1‑90 (MQ=255)
tCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAcc > 2:678257/1‑90 (MQ=255)
tCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAcc > 1:299532/1‑90 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc < 1:312145/90‑1 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc < 1:423831/90‑1 (MQ=255)
aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc < 1:678257/90‑1 (MQ=255)
ctctTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc < 2:269336/51‑1 (MQ=255)
ctctTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc > 1:269336/1‑51 (MQ=255)
ctctTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCctgctg > 2:783778/1‑90 (MQ=255)
aaCGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCt < 2:609146/90‑1 (MQ=255)
gCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCa > 1:815699/1‑90 (MQ=255)
gACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTTAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCg > 1:26114/1‑90 (MQ=255)
ccGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTCCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCa < 1:34818/90‑1 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 1:803693/90‑1 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 1:835478/90‑1 (MQ=255)
cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag < 1:326480/90‑1 (MQ=255)
cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag < 1:598870/90‑1 (MQ=255)
cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag > 1:285559/1‑90 (MQ=255)
cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag < 1:480333/90‑1 (MQ=255)
cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag < 2:351937/90‑1 (MQ=255)
cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag < 1:407956/90‑1 (MQ=255)
cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag < 1:114998/90‑1 (MQ=255)
gTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACg > 1:413956/1‑90 (MQ=255)
|
CGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACG > NZ_CP009273/2814181‑2814351
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTGTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > NZ_CP009273/2814169‑2814354
|
GTGTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGG > SRR3722079.248845/1‑100 (MQ=60)
GTGTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGG < SRR3722079.621205/100‑1 (MQ=60)
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCA > SRR3722079.472286/1‑100 (MQ=60)
GTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCACCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCA < SRR3722079.813924/100‑1 (MQ=60)
CAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGT > SRR3722079.236281/1‑100 (MQ=60)
CAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGT > SRR3722079.771263/1‑100 (MQ=60)
GTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCT < SRR3722079.575853/100‑1 (MQ=60)
ACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGC < SRR3722079.787874/100‑1 (MQ=60)
CCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCA > SRR3722079.244618/1‑100 (MQ=60)
ATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACC > SRR3722079.301985/1‑100 (MQ=60)
AGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCC < SRR3722079.427485/100‑1 (MQ=60)
AGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCC < SRR3722079.685377/100‑1 (MQ=60)
AGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCC < SRR3722079.314675/100‑1 (MQ=60)
GTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCctgtctcttatacacatctccgagcccac > SRR3722079.271591/1‑71 (MQ=60)
ATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCA > SRR3722079.824446/1‑100 (MQ=60)
AGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTTAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCG > SRR3722079.26297/1‑100 (MQ=60)
CGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAG > SRR3722079.287927/1‑100 (MQ=60)
CCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTCCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAA < SRR3722079.35070/100‑1 (MQ=60)
CGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAAC < SRR3722079.329097/100‑1 (MQ=60)
CGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAAC < SRR3722079.812316/100‑1 (MQ=60)
CGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAAC < SRR3722079.844420/100‑1 (MQ=60)
GCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACG > SRR3722079.417514/1‑100 (MQ=60)
CGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGT < SRR3722079.115942/100‑1 (MQ=60)
CGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGT < SRR3722079.411429/100‑1 (MQ=60)
CGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGT < SRR3722079.484539/100‑1 (MQ=60)
CGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGT < SRR3722079.604888/100‑1 (MQ=60)
CTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > SRR3722079.627493/1‑100 (MQ=60)
|
GTGTCGTACAGACGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACGTCG > NZ_CP009273/2814169‑2814354
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
