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 |
2,940,645 |
C→T |
intergenic (‑108/‑101) |
mltA ← / → BW25113_RS14635 |
murein transglycosylase A/tRNA‑Met |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,940,645 | 0 | C | T | 85.7%
| 72.7
/ 3.6
| 28 | intergenic (‑108/‑101) | mltA/BW25113_RS14635 | murein transglycosylase A/tRNA‑Met |
| Reads supporting (aligned to +/- strand): ref base C (1/3); new base T (7/17); total (8/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.51e-01 |
TAAGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAG > NZ_CP009273/2940562‑2940726
|
tAAGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGt > 2:374518/1‑90 (MQ=255)
aaGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTg > 1:557183/1‑90 (MQ=255)
gcgTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCaa < 2:445300/90‑1 (MQ=255)
cgTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCaaa < 2:327518/90‑1 (MQ=255)
gTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAAt > 2:54503/1‑90 (MQ=255)
aaatgaGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATc < 1:58623/90‑1 (MQ=255)
gcagcCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTa < 1:140325/90‑1 (MQ=255)
cccTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAgg > 1:507859/1‑90 (MQ=255)
gACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGc > 2:86324/1‑90 (MQ=255)
gACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGc > 2:370477/1‑90 (MQ=255)
gACGCAAATTTTGCACAAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGc > 2:91920/1‑90 (MQ=255)
cAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGcc > 2:562029/1‑55 (MQ=255)
cAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGcc < 1:562029/55‑1 (MQ=255)
ttGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAAcgc < 2:553425/90‑1 (MQ=255)
tGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAAcgcg < 1:192570/90‑1 (MQ=255)
tGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAAcgcg < 2:40750/90‑1 (MQ=255)
cacaAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAg < 2:501645/90‑1 (MQ=255)
cacaAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAg < 2:557183/90‑1 (MQ=255)
cacaAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAg < 1:461345/90‑1 (MQ=255)
caAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCg < 2:317572/90‑1 (MQ=255)
aaaaaaTAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCgg < 2:372462/90‑1 (MQ=255)
aaaaaaTAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCgg < 2:138528/90‑1 (MQ=255)
aaaaaaTAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCgg < 1:523064/90‑1 (MQ=255)
aaaaaaTAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCgg < 1:363158/90‑1 (MQ=255)
aaaaaaTAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCgg < 2:218623/90‑1 (MQ=255)
aaaaaaTAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCgg < 1:91920/90‑1 (MQ=255)
aaaaTAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAg < 2:108663/90‑1 (MQ=255)
aaaaTAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAg < 1:208078/90‑1 (MQ=255)
|
TAAGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAG > NZ_CP009273/2940562‑2940726
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
GTTAAAAAATAAGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGC > NZ_CP009273/2940553‑2940736
|
GTTAAAAAATAAGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTG > SRR3722112.565626/1‑100 (MQ=60)
agcgtcagatgtgtataagagacagCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGA < SRR3722112.570554/75‑1 (MQ=60)
AAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAA < SRR3722112.59335/100‑1 (MQ=60)
AGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGG > SRR3722112.515254/1‑100 (MQ=60)
GCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGT < SRR3722112.142079/100‑1 (MQ=60)
TGCACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTAT < SRR3722112.194923/100‑1 (MQ=60)
CACAAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAG < SRR3722112.467876/100‑1 (MQ=60)
AAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGC < SRR3722112.367812/100‑1 (MQ=60)
AAAAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGC < SRR3722112.530774/100‑1 (MQ=60)
AAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGC < SRR3722112.93073/100‑1 (MQ=60)
AAAATAGGTTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGC < SRR3722112.210599/100‑1 (MQ=60)
|
GTTAAAAAATAAGGCGCAACGAAGATAACAAACCGCCGCGTTTAATGAAATGAGCAGCCTCTCCCTGACGCAAATTTTGCACAAAAAATAGGCTTTAGTGATTTGTTTTTGTTCAAAATCATGCCAAATCCGTGATCGGGGTAAAAAAAAGGTTGCATGAAAACGCGAGCGGAGTATAGTGCGC > NZ_CP009273/2940553‑2940736
|
| 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: ‑ |
