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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,060,988 |
(A)6→5 |
intergenic (+240/‑53) |
yccE → / → agp |
YccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,060,983 | 0 | A | . | 100.0%
| 77.1
/ NA
| 19 | intergenic (+235/‑58) | yccE/agp | YccE family protein/bifunctional glucose‑1‑phosphatase/inositol phosphatase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (9/10); total (9/10) |
GCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGC > NZ_CP009273/1060904‑1061066
|
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 1:161794/1‑90 (MQ=255)
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 1:432696/1‑90 (MQ=255)
gCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCata > 2:372759/1‑90 (MQ=255)
cAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTc < 1:510694/90‑1 (MQ=255)
ttGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTcac < 2:86801/90‑1 (MQ=255)
ttGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTcac < 2:449739/90‑1 (MQ=255)
gCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCacac < 2:432696/90‑1 (MQ=255)
ttttGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTa > 2:226655/1‑90 (MQ=255)
gATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGtgattg < 1:372759/90‑1 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAag > 2:91241/1‑90 (MQ=255)
gAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAag > 2:505242/1‑90 (MQ=255)
aaaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTca > 2:460758/1‑62 (MQ=255)
aaaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTca < 1:460758/62‑1 (MQ=255)
aaaCAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAgg > 1:56680/1‑90 (MQ=255)
aGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGcc < 2:327959/90‑1 (MQ=255)
ccTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATcgccg < 1:480547/90‑1 (MQ=255)
gTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCttt < 2:288456/36‑1 (MQ=38)
gTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCttt > 1:288456/1‑36 (MQ=38)
ttCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGc < 1:226655/90‑1 (MQ=255)
|
GCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGC > NZ_CP009273/1060904‑1061066
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGGG > NZ_CP009273/1060894‑1061076
|
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATA > SRR3722092.164505/1‑100 (MQ=60)
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATA > SRR3722092.441131/1‑100 (MQ=60)
CAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTC < SRR3722092.520941/100‑1 (MQ=60)
gatgtgtataagagacagTGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAG < SRR3722092.469858/82‑1 (MQ=60)
atctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGA < SRR3722092.63442/51‑1 (MQ=60)
GATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAG < SRR3722092.379787/100‑1 (MQ=60)
GTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGG > SRR3722092.57601/1‑100 (MQ=60)
TTGCGAACCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATctgtctcttatacacatctgacgctgccgacgaccatcttagtg > SRR3722092.293444/1‑56 (MQ=60)
CCTGTTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGC < SRR3722092.490094/100‑1 (MQ=60)
TTCCCGG‑AAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGGG < SRR3722092.230361/100‑1 (MQ=60)
|
GGCATAGTTTGCGTCAAACCTTGCCTGTTTTTGAAGATGTATATAGAAAAACAGGCGTTCAACAAGCCATTTTGCGAACCTGTTCCCGGAAAAAAGTCATATTTCTGTCACACTCTTTAGTGATTGATAACAAAAGAGGTGCCAGGAATGAACAAAACGCTAATCGCCGCAGCTGTGGCAGGG > NZ_CP009273/1060894‑1061076
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
