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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,807,028 |
T→C |
E121G (GAA→GGA) |
BW25113_RS09050 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,807,028 | 0 | T | C | 92.9%
| 35.4
/ ‑3.0
| 14 | E121G (GAA→GGA) | BW25113_RS09050 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (7/6); total (8/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.60e-01 |
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAA > NZ_CP009273/1806945‑1807105
|
gTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGc < 1:275527/90‑1 (MQ=255)
atataATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa < 1:212611/90‑1 (MQ=255)
atataATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa < 1:244380/90‑1 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCa > 2:535470/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 2:572271/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:138339/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:18494/1‑90 (MQ=255)
gTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCttt > 2:211302/1‑90 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGa > 1:7249/1‑58 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGa < 2:7249/58‑1 (MQ=255)
aaccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACct > 1:432451/1‑90 (MQ=255)
ccTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACctct > 2:300754/1‑90 (MQ=255)
tGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCAc < 2:338928/90‑1 (MQ=255)
ttGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATaa < 1:505327/90‑1 (MQ=255)
|
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAA > NZ_CP009273/1806945‑1807105
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTCCCGACAGGATGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAA > NZ_CP009273/1806932‑1807115
|
CTCCCGACAGGATGTATATAATTTTGTTCATAGTGTATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTG < SRR3722112.432449/100‑1 (MQ=60)
GTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGA < SRR3722112.278741/100‑1 (MQ=60)
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAG < SRR3722112.215180/100‑1 (MQ=60)
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAG < SRR3722112.247277/100‑1 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722112.140067/1‑100 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722112.18726/1‑100 (MQ=60)
GTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCctgtctcttatacacatctgac > SRR3722112.7338/1‑78 (MQ=60)
GTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCT > SRR3722112.438343/1‑100 (MQ=60)
GATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcgg > SRR3722112.245976/1‑46 (MQ=60)
TTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAA < SRR3722112.512679/100‑1 (MQ=60)
|
CTCCCGACAGGATGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGATTATTAA > NZ_CP009273/1806932‑1807115
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
