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 |
3,477,291 |
+GC |
pseudogene (63/1363 nt) |
tdcG ← |
L‑serine ammonia‑lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,477,291 | 1 | . | G | 100.0%
| 119.5
/ NA
| 35 | pseudogene (63/1363 nt) | tdcG | L‑serine ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (11/24); total (11/24) |
| * | NC_017635 | 3,477,291 | 2 | . | C | 100.0%
| 119.9
/ NA
| 35 | pseudogene (63/1363 nt) | tdcG | L‑serine ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (11/24); total (11/24) |
AGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAAT > NC_017635/3477244‑3477326
||
aGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTg < 2:2265026/48‑1 (MQ=255)
gCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTgg > 2:2632652/1‑47 (MQ=255)
ccGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTggc > 1:2022270/1‑46 (MQ=255)
ccGCTACCTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTggc < 2:1828394/48‑3 (MQ=39)
cGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑gcc < 1:1805815/48‑1 (MQ=255)
cGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑gcc < 2:1234048/48‑1 (MQ=255)
cTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑gcccc < 1:2420777/48‑3 (MQ=39)
tCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGt < 1:1527937/47‑1 (MQ=37)
tCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGt < 2:1943424/47‑1 (MQ=37)
tCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGt < 2:1533047/47‑1 (MQ=37)
tCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGt < 2:1124394/47‑1 (MQ=37)
ccAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTa < 2:388197/47‑1 (MQ=37)
ccGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCg > 1:1955204/1‑47 (MQ=37)
ccGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGa < 2:1957323/48‑1 (MQ=37)
cGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGaa < 2:2234444/48‑1 (MQ=37)
aTCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACt < 2:2169271/48‑1 (MQ=37)
tCAATAAAACTTTTTCCGTCATTCATTGGCCCCACGGTATGCGAACTg > 1:1196179/1‑48 (MQ=255)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:2613791/1‑48 (MQ=37)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:1719165/1‑48 (MQ=37)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:2510203/1‑48 (MQ=37)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 2:2204132/1‑48 (MQ=37)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:635872/1‑48 (MQ=37)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:51401/1‑48 (MQ=37)
tCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 2:2383866/1‑48 (MQ=37)
cAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:1597381/1‑47 (MQ=37)
aaTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTgg < 2:1500951/47‑1 (MQ=37)
aaaCTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAggg < 2:890844/47‑1 (MQ=37)
aaaCTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGa < 1:1740601/48‑1 (MQ=37)
aCTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGAcc < 1:2423634/48‑1 (MQ=37)
cTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCa < 1:862728/48‑1 (MQ=25)
cTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCa < 1:440295/48‑1 (MQ=25)
cTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCa < 2:2624241/48‑1 (MQ=25)
cTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCa < 1:404802/48‑1 (MQ=25)
cTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCa < 2:733974/48‑1 (MQ=25)
cTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCa < 2:973224/48‑1 (MQ=25)
tttCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAt < 2:2494184/47‑1 (MQ=25)
tttCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAt < 1:396364/47‑1 (MQ=25)
tttCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAt < 1:303773/47‑1 (MQ=25)
ttCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATc < 2:2262901/47‑1 (MQ=25)
cGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCa < 2:1615933/47‑1 (MQ=21)
cGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCa < 1:1804764/47‑1 (MQ=21)
ggCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAt > 2:1116525/1‑48 (MQ=21)
||
AGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAAT > NC_017635/3477244‑3477326
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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
ATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > NC_017635/3477241‑3477335
|
ATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG < M01420:84:000000000‑ABVEH:1:1104:6164:15160/51‑1 (MQ=60)
AGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑GCC > M01420:84:000000000‑ABVEH:1:2104:7752:9661/1‑51 (MQ=60)
CCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGgcccc < M01420:84:000000000‑ABVEH:1:2102:13889:12314/51‑6 (MQ=60)
GCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCAC < M01420:84:000000000‑ABVEH:1:2107:23576:19263/51‑1 (MQ=60)
TTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTAT < M01420:84:000000000‑ABVEH:1:1113:16622:28960/50‑1 (MQ=60)
AGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGA > M01420:84:000000000‑ABVEH:1:2103:26388:18885/1‑50 (MQ=60)
GCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAAC < M01420:84:000000000‑ABVEH:1:2111:17311:20039/51‑1 (MQ=60)
GATCAATAAAACTTTTTCCGTCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:1111:26569:8937/1‑51 (MQ=47)
GATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:1101:7762:14121/1‑51 (MQ=60)
GATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:2109:20529:10972/1‑51 (MQ=60)
GATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:2108:21217:13899/1‑51 (MQ=60)
GATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:1106:15856:14541/1‑51 (MQ=60)
GATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:2101:2038:17710/1‑51 (MQ=60)
ATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:84:000000000‑ABVEH:1:1114:21163:16998/1‑50 (MQ=60)
CAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGG < M01420:84:000000000‑ABVEH:1:2114:12607:15919/51‑1 (MQ=60)
AAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACC < M01420:84:000000000‑ABVEH:1:2101:15337:22038/51‑1 (MQ=60)
AACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAA < M01420:84:000000000‑ABVEH:1:2107:21806:19815/51‑1 (MQ=60)
ACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAT < M01420:84:000000000‑ABVEH:1:1108:19820:13077/51‑1 (MQ=60)
ACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAT < M01420:84:000000000‑ABVEH:1:1104:25990:14961/51‑1 (MQ=60)
ACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAT < M01420:84:000000000‑ABVEH:1:1104:10841:21983/51‑1 (MQ=60)
ACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAAT < M01420:84:000000000‑ABVEH:1:2109:13164:23750/51‑1 (MQ=60)
TTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCC < M01420:84:000000000‑ABVEH:1:1104:16772:13338/50‑1 (MQ=60)
TTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCC < M01420:84:000000000‑ABVEH:1:1103:8544:17976/50‑1 (MQ=60)
CCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAT < M01420:84:000000000‑ABVEH:1:2102:21943:12117/50‑1 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGGCCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2102:15923:18016/1‑50 (MQ=44)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCCATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1112:12359:12808/1‑50 (MQ=44)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAGTTTTGA > M01420:84:000000000‑ABVEH:1:1107:2678:19056/1‑50 (MQ=44)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2109:25950:15069/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1101:15529:3141/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1108:5754:17647/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2106:15028:28911/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2105:19146:10984/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1101:11178:15917/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2104:8871:13024/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2103:6699:23075/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2103:25251:20473/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:2103:21073:17419/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1105:23006:14467/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1107:10720:24397/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1114:11388:12221/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1108:12133:16480/1‑50 (MQ=60)
ATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGA > M01420:84:000000000‑ABVEH:1:1112:15542:7067/1‑50 (MQ=60)
CATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT < M01420:84:000000000‑ABVEH:1:2107:23703:19984/51‑1 (MQ=60)
CATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:84:000000000‑ABVEH:1:1103:21622:8295/1‑51 (MQ=60)
ATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:84:000000000‑ABVEH:1:2107:23201:25872/1‑50 (MQ=60)
ATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:84:000000000‑ABVEH:1:2111:12918:12056/1‑50 (MQ=60)
ATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:84:000000000‑ABVEH:1:1113:12760:16566/1‑50 (MQ=60)
ATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:84:000000000‑ABVEH:1:2111:4488:17193/1‑50 (MQ=60)
|
ATAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > NC_017635/3477241‑3477335
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
