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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,739,096 |
T→C |
E61G (GAA→GGA) |
rimM ← |
ribosome maturation factor RimM |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,739,096 | 0 | T | C | 94.7%
| 51.7
/ ‑3.1
| 19 | E61G (GAA→GGA) | rimM | ribosome maturation factor RimM |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (8/10); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 4.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.31e-01 |
CACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGT > NZ_CP009273/2739010‑2739175
|
cacaATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCttccagcttccca < 1:174946/90‑1 (MQ=255)
cacaATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCttccagcttccca < 2:336771/90‑1 (MQ=255)
cGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTc < 2:121535/90‑1 (MQ=255)
cGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTc < 1:175253/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:365406/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 1:60589/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 2:314870/90‑1 (MQ=255)
gTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt > 2:310363/1‑90 (MQ=255)
gCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGAt > 2:22094/1‑90 (MQ=255)
gCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGAt < 2:65337/90‑1 (MQ=255)
ttGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAg > 1:81736/1‑90 (MQ=255)
ttGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAg < 1:310363/90‑1 (MQ=255)
tgatgaTCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGt > 1:409311/1‑90 (MQ=255)
tCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCaaaaa < 2:188128/90‑1 (MQ=255)
cATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAAt > 2:119898/1‑90 (MQ=255)
ccTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCttt > 2:22723/1‑90 (MQ=255)
ccTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt < 1:290637/61‑1 (MQ=255)
ccTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGAt > 2:290637/1‑61 (MQ=255)
gATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCgg < 1:1107/90‑1 (MQ=255)
tggtgCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCt > 1:397791/1‑90 (MQ=255)
cTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGt > 2:294756/1‑90 (MQ=255)
|
CACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGT > NZ_CP009273/2739010‑2739175
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
GACAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGT > NZ_CP009273/2739002‑2739175
|
GACAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGC < SRR3722114.367652/100‑1 (MQ=60)
CACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTG < SRR3722114.176688/100‑1 (MQ=60)
CGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACC < SRR3722114.176997/100‑1 (MQ=60)
agatgtgtataagagacaGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGC < SRR3722114.293719/82‑1 (MQ=60)
GTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGC < SRR3722114.61190/100‑1 (MQ=60)
GCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAG > SRR3722114.82602/1‑100 (MQ=60)
CCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGT > SRR3722114.414318/1‑100 (MQ=60)
TTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGC < SRR3722114.313670/100‑1 (MQ=60)
GTCCTGATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCT > SRR3722114.402621/1‑100 (MQ=60)
GATTGTGGTGCTTCCAGCTTCCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGT < SRR3722114.1119/100‑1 (MQ=60)
|
GACAATTTCACAATTCGTCAGCAGGTTCGCCGCATCACGATCGTCAACGCCTTTCAGCTTGATGATCATGTCCTGATTGTGGTGCTTCCAGCTTTCCAGCTGGACTTGCTGCCACTGACCCGCCTTCTGGATAAACCAGGGCTGATAGTCAAAAATGCTTTCGGCGTCTTCGGT > NZ_CP009273/2739002‑2739175
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
