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 F1 I1 R1
|
66 |
46.7 |
5280542 |
98.1% |
5180211 |
47.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,158,013 |
+T |
coding (522/2247 nt) |
ptsP ← |
phosphoenolpyruvate‑‑protein phosphotransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,158,012 | 1 | . | T | 100.0%
| 109.2
/ NA
| 29 | P175T (CCG→ACG) | ptsP | phosphoenolpyruvate‑‑protein phosphotransferase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (16/13); total (16/13) |
GGCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑TAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGG > NC_017635/3157968‑3158053
|
ggCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑tt > 2:1331631/1‑46 (MQ=255)
gCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑tta < 2:2374774/47‑3 (MQ=255)
gCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑tta < 2:1784256/47‑3 (MQ=255)
ccTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATgcg > 2:227410/1‑48 (MQ=38)
ccTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATgcg > 1:2469354/1‑48 (MQ=38)
ccTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATgcg > 1:2585337/1‑48 (MQ=38)
ccAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGCgg < 2:1232574/47‑1 (MQ=38)
cTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTcgc > 1:2367330/1‑48 (MQ=39)
cGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGt < 1:1585965/47‑1 (MQ=39)
aTCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCg < 2:1974111/48‑1 (MQ=39)
aTCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCg < 1:2143822/48‑1 (MQ=39)
tCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGa > 1:242269/1‑48 (MQ=39)
tCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGa > 2:382596/1‑48 (MQ=39)
gCCACACCAGGTGCTGCTGGTTAATGCGCGGATTCGCGTCTGGCGata < 1:2627660/48‑1 (MQ=37)
gCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGata < 1:2288387/48‑1 (MQ=39)
gCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGata < 1:216990/48‑1 (MQ=39)
gCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGata < 1:1006373/48‑1 (MQ=39)
gCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGat < 1:449732/47‑1 (MQ=39)
gCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGat < 2:2592229/47‑1 (MQ=39)
gCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGat < 2:2571465/47‑1 (MQ=39)
cacaCCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATAtt > 1:58058/1‑48 (MQ=39)
cacCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGc < 2:424740/48‑1 (MQ=39)
cacCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGc < 2:168379/48‑1 (MQ=39)
acCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGcc > 1:2014918/1‑48 (MQ=39)
acCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGcc > 1:1918152/1‑48 (MQ=39)
cAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGccc > 1:1504147/1‑47 (MQ=39)
gTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCaaa > 2:1351242/1‑47 (MQ=39)
gTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCaaa > 2:1344612/1‑47 (MQ=39)
tgctgcCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCaaa > 2:2337900/1‑46 (MQ=39)
tgcCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAggg > 2:2085186/1‑48 (MQ=255)
tgcCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAggg > 1:956310/1‑48 (MQ=255)
tgcCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAggg > 1:2607826/1‑48 (MQ=255)
|
GGCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑TAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGG > NC_017635/3157968‑3158053
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACGTGGCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑TAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGCAGTCAAC > NC_017635/3157963‑3158061
|
AACGTGGCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑T < M01420:84:000000000‑ABVEH:1:2112:19933:19175/51‑1 (MQ=60)
GGCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑Ttatt < M01420:84:000000000‑ABVEH:1:2112:11413:5973/50‑5 (MQ=60)
ATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGC > M01420:84:000000000‑ABVEH:1:2112:22241:5050/1‑51 (MQ=60)
ATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGC > M01420:84:000000000‑ABVEH:1:2109:7408:4704/1‑51 (MQ=60)
ATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGC > M01420:84:000000000‑ABVEH:1:2108:13877:5468/1‑51 (MQ=60)
GCCTTCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCG > M01420:84:000000000‑ABVEH:1:2107:5968:9183/1‑51 (MQ=60)
TCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCT < M01420:84:000000000‑ABVEH:1:2114:25242:20091/50‑1 (MQ=60)
TCGGCAATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCT < M01420:84:000000000‑ABVEH:1:1114:24765:14883/50‑1 (MQ=60)
AATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGAT > M01420:84:000000000‑ABVEH:1:1103:10403:5431/1‑51 (MQ=60)
AATCGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGAT < M01420:84:000000000‑ABVEH:1:2105:28532:11031/51‑1 (MQ=60)
CGCCACACCAGGTGCTGCTGGTTAATGCGCGGATTCGCGTCTGGCGATATT < M01420:84:000000000‑ABVEH:1:2109:5105:13562/51‑1 (MQ=54)
CGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATT < M01420:84:000000000‑ABVEH:1:1102:19726:24214/51‑1 (MQ=60)
CGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATT < M01420:84:000000000‑ABVEH:1:2106:25658:16520/51‑1 (MQ=60)
CGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATT < M01420:84:000000000‑ABVEH:1:1109:26632:17990/51‑1 (MQ=60)
CGCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATAT < M01420:84:000000000‑ABVEH:1:1104:15878:24087/50‑1 (MQ=60)
GCCACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTG > M01420:84:000000000‑ABVEH:1:1101:14998:15406/1‑51 (MQ=60)
ACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCC > M01420:84:000000000‑ABVEH:1:2104:11844:8099/1‑51 (MQ=60)
ACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCC > M01420:84:000000000‑ABVEH:1:2103:7664:11810/1‑51 (MQ=60)
ACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCC > M01420:84:000000000‑ABVEH:1:2111:4310:21576/1‑51 (MQ=60)
ACACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCC > M01420:84:000000000‑ABVEH:1:2114:7035:19345/1‑51 (MQ=60)
ACCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCA > M01420:84:000000000‑ABVEH:1:1113:5688:22224/1‑50 (MQ=60)
CCAGGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAA > M01420:84:000000000‑ABVEH:1:2112:3827:9015/1‑50 (MQ=60)
GGTGCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAAC > M01420:84:000000000‑ABVEH:1:2114:13089:24171/1‑49 (MQ=60)
GCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGC > M01420:84:000000000‑ABVEH:1:2109:7960:9826/1‑51 (MQ=60)
GCTGCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGC > M01420:84:000000000‑ABVEH:1:1109:26314:8300/1‑51 (MQ=60)
GCCGGTTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGCAGT < M01420:84:000000000‑ABVEH:1:2109:6036:5701/51‑1 (MQ=60)
ggtTAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGCAGTCA > M01420:84:000000000‑ABVEH:1:1104:9611:25125/4‑50 (MQ=60)
GT‑TAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGCAGTCAAC > M01420:84:000000000‑ABVEH:1:2106:19472:22182/1‑51 (MQ=60)
|
AACGTGGCATCCTGCCAGCCTTCGGCAATCGCCACACCAGGTGCTGCCGG‑TAATGCGCGGATTCGCGTCTGGCGATATTGCCCAAACAGGGCAGTCAAC > NC_017635/3157963‑3158061
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
