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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
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 | 90.5%
| 58.2
/ ‑0.2
| 21 | I193V (ATT→GTT) | yibB | protein YibB |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (13/6); total (14/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
TTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > NZ_CP009273/3786384‑3786551
|
ttCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGaa > 1:354392/1‑90 (MQ=255)
aCTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCaaaa < 2:276169/90‑1 (MQ=255)
aTTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAATTCAAAAACCt < 2:323290/90‑1 (MQ=255)
aaTTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTga < 1:81099/90‑1 (MQ=255)
tgtgAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑t < 2:5346/90‑1 (MQ=255)
gtgAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑tt > 2:346061/1‑90 (MQ=255)
tGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGaa < 2:262194/90‑1 (MQ=255)
tataCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACtt > 1:139696/1‑90 (MQ=255)
tataCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACtt > 2:272146/1‑90 (MQ=255)
tataCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACtt > 1:2912/1‑90 (MQ=255)
aCATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTtca > 2:363522/1‑90 (MQ=255)
cATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTtcat > 1:62701/1‑90 (MQ=255)
tGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTtcatca > 2:291686/1‑90 (MQ=255)
gATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAg < 2:14542/49‑1 (MQ=255)
gATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAg > 1:14542/1‑49 (MQ=255)
gATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTTATAGTGAAAAGATGCATCTTACTTtcatca > 2:209464/1‑90 (MQ=255)
aTTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCaaa > 1:38952/1‑90 (MQ=255)
ttGCCAATCATGAAATCAAAAACCTGTTGTTgaga < 1:330081/35‑1 (MQ=255)
ttGCCAATCATGAAATCAAAAACCTGTTGTTgaga > 2:330081/1‑35 (MQ=255)
ttGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAt > 1:107300/1‑90 (MQ=255)
gCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATgg > 1:302035/1‑90 (MQ=255)
|
TTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCC‑TTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > NZ_CP009273/3786384‑3786551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > NZ_CP009273/3786374‑3786551
|
TTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAA > SRR3722090.359007/1‑100 (MQ=60)
AATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAG < SRR3722090.81992/100‑1 (MQ=60)
gatgctcaggagtctcgtgggctcggagatgtgtataagagacagATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTA < SRR3722090.334371/55‑1 (MQ=60)
CCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTT > SRR3722090.141155/1‑100 (MQ=60)
CCCAATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTT > SRR3722090.2939/1‑100 (MQ=60)
ATAATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCAT > SRR3722090.63375/1‑100 (MQ=60)
ATATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTctgtctcttatacacatctccgagcccacga > SRR3722090.14699/1‑69 (MQ=60)
TATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAA > SRR3722090.39352/1‑100 (MQ=60)
ATATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAAT > SRR3722090.108450/1‑100 (MQ=60)
ATACATGATTGCCAACCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > SRR3722090.305879/1‑100 (MQ=60)
|
TTTTTTGACTTTCCAGAACTAATTTATAGAATTCTTTCCATTTATGCTGTGAACCAACAATTGCGCCCCCAATAATATATACATGATTGCCAATCATGAAATCAAAAACCTGTTGTTGAGATGTGACAGTAAGCCCTTTTTTTATAGTGAAAAGATGCATCTTACTTTCATCAAATGG > NZ_CP009273/3786374‑3786551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
