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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,786,467 |
T→C |
I193V (ATT→GTT) |
yibB ← |
protein YibB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,786,467 | 0 | T | C | 100.0%
| 57.9
/ NA
| 18 | I193V (ATT→GTT) | yibB | protein YibB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/6); total (12/6) |
TTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAT > NZ_CP009273/3786384‑3786549
|
ttCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGaa < 1:109620/90‑1 (MQ=255)
aaTTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAAcc > 2:425386/1‑90 (MQ=255)
aaTTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAAcc > 2:111771/1‑90 (MQ=255)
ttATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCtgt < 1:153481/90‑1 (MQ=255)
tttATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGt > 1:43047/1‑90 (MQ=255)
tgtgAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCt < 2:55150/90‑1 (MQ=255)
gtgAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCtt > 1:387893/1‑90 (MQ=255)
tgAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCttt > 1:428732/1‑90 (MQ=255)
gcCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGaaaa < 2:127446/89‑1 (MQ=255)
gcCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGaaaa > 1:127446/1‑89 (MQ=255)
tataCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACtt > 2:332033/1‑90 (MQ=255)
tataCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACtt > 1:235569/1‑90 (MQ=255)
taCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTtc > 2:201424/1‑90 (MQ=255)
cATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCt < 1:375237/56‑1 (MQ=255)
cATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCt > 2:375237/1‑56 (MQ=255)
ttGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAt > 2:336017/1‑90 (MQ=255)
gCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTAc > 1:340946/1‑77 (MQ=255)
gCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTAc < 2:340946/77‑1 (MQ=255)
|
TTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAT > NZ_CP009273/3786384‑3786549
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
GTGTTATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > NZ_CP009273/3786368‑3786551
|
gaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagCAACAATTGCGCCCCCAATAATATATACATGATTGCCAAC < SRR3722087.383860/40‑1 (MQ=60)
GTGTTATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAAC < SRR3722087.431280/100‑1 (MQ=60)
TTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACC < SRR3722087.110681/100‑1 (MQ=60)
TTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATG < SRR3722087.154886/100‑1 (MQ=60)
ATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGT > SRR3722087.43391/1‑100 (MQ=60)
CATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTT > SRR3722087.392372/1‑100 (MQ=60)
ATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTT > SRR3722087.433737/1‑100 (MQ=60)
ctcggagatgtgtataagagacagATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAG < SRR3722087.379545/76‑1 (MQ=60)
CAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAG > SRR3722087.128642/1‑100 (MQ=60)
CCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTT > SRR3722087.237750/1‑100 (MQ=60)
ATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAActg > SRR3722087.344749/1‑97 (MQ=60)
|
GTGTTATTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > NZ_CP009273/3786368‑3786551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
