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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,797,377 |
(T)5→4 |
coding (517/960 nt) |
nrdF → |
class 1b ribonucleoside‑diphosphate reductase subunit beta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,797,373 | 0 | T | . | 94.4%
| 62.8
/ ‑1.3
| 18 | coding (513/960 nt) | nrdF | class 1b ribonucleoside‑diphosphate reductase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (5/12); total (5/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT > NZ_CP009273/2797290‑2797456
|
ggTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTAttttcca > 1:33896/1‑87 (MQ=255)
gTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTAttttccag > 1:63857/1‑86 (MQ=255)
gCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAg > 1:8603/1‑90 (MQ=255)
cTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGc < 1:589253/90‑1 (MQ=255)
aaaGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGAcc < 1:453013/90‑1 (MQ=255)
gAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAAt < 2:269659/90‑1 (MQ=255)
tCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACcgc < 2:511564/90‑1 (MQ=255)
tCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACcgc < 2:28712/90‑1 (MQ=255)
aGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGAcc < 1:472990/90‑1 (MQ=255)
ttGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTc < 1:232586/90‑1 (MQ=255)
aTTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGc > 1:469764/1‑90 (MQ=255)
aTTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGc < 2:471209/90‑1 (MQ=255)
aTTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGc < 2:50524/90‑1 (MQ=255)
tttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCAc < 2:268933/90‑1 (MQ=255)
ttCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACg < 1:443526/90‑1 (MQ=255)
cTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGt > 1:443860/1‑90 (MQ=255)
cTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGt > 1:135452/1‑90 (MQ=255)
ggCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTta < 1:407549/90‑1 (MQ=255)
gCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTtactac > 2:477790/1‑90 (MQ=255)
cGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAt < 1:141174/90‑1 (MQ=255)
|
GGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT > NZ_CP009273/2797290‑2797456
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ 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
ACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA > NZ_CP009273/2797280‑2797466
|
ACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCA > SRR3722109.34294/1‑100 (MQ=60)
CATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAG > SRR3722109.64616/1‑100 (MQ=60)
GTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAG > SRR3722109.8720/1‑100 (MQ=60)
CTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATAC < SRR3722109.598171/100‑1 (MQ=60)
AAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGG < SRR3722109.459799/100‑1 (MQ=60)
AGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCT < SRR3722109.480119/100‑1 (MQ=60)
TTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCG < SRR3722109.235340/100‑1 (MQ=60)
TTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGC > SRR3722109.476843/1‑100 (MQ=60)
ATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGT > SRR3722109.137126/1‑100 (MQ=60)
ATTCCGGTTTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGT > SRR3722109.450457/1‑100 (MQ=60)
TTCTGGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACAT < SRR3722109.450119/100‑1 (MQ=60)
GGCTGCCGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGC < SRR3722109.413480/100‑1 (MQ=60)
CGATGTA‑TTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA < SRR3722109.142926/100‑1 (MQ=60)
|
ACATTATCGCGGTGATGATCCGCTGAAAAAGAAAATCGCCAGTGTGTTTCTTGAATCTTTTTTGTTCTATTCCGGTTTCTGGCTGCCGATGTATTTTTCCAGCCGCGGAAAGCTGACCAATACCGCGGACCTGATCCGTCTGATTATCCGCGATGAAGCAGTCCACGGTTACTACATAGGCTATAAA > NZ_CP009273/2797280‑2797466
|
| 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: ‑ |
