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 |
|
A20 F4 I5 R1
|
61 |
40.1 |
2005705 |
98.2% |
1969602 |
131.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AE015451_phaM1 |
5,555,608 |
+GCC |
intergenic (‑84/+87) |
PP_4887 CDS (conserved protein of unknown function) ← / ← PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) |
–/– |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AE015451_phaM1 | 5,555,608 | 1 | . | G | 100.0%
| 41.4
/ NA
| 13 | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (0/13); total (0/13) |
| * | AE015451_phaM1 | 5,555,608 | 2 | . | C | 100.0%
| 41.3
/ NA
| 13 | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (0/13); total (0/13) |
| * | AE015451_phaM1 | 5,555,608 | 3 | . | C | 100.0%
| 41.3
/ NA
| 13 | intergenic (‑84/+87) | PP_4887 CDS (conserved protein of unknown function)/PP_4888 CDS (putative methyl‑accepting chemotaxis transducer) | –/– |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (0/13); total (0/13) |
CTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGG > AE015451_phaM1/5555469‑5555643
|||
cTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTATTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccc < 2:53396/144‑5 (MQ=255)
tttgCAGGAAATTCAGTTCGGCCTGGGCAGCGATTAGTTGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGAAACACCGCTCAGGTGTGGGAGCGGCCTGGTGTCGCGAAAGGGCCGCATAgcggcccc < 2:302964/142‑6 (MQ=255)
tgtgCAGGAAATTCAGTTCGGCCTGGGCAGCGGTTATTCGGGCGGACAGGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCAGAGCAACACCGCTCAGGTGTGGGAGCGGCTTTGTGTCGCGAAAGGGCCGCAGAgcggcccc < 2:302961/144‑6 (MQ=38)
tgtgCAGGAAATTCAGTTCGGCCTGGGCAGCGATTAGTCGGGCGGACAGGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggcccc < 2:302963/144‑6 (MQ=255)
tgtgCAGGAAATTCAGTTCGGCCTGGCCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGTGGCCTTGTGTCGCGAAAGGGCCGCAGAgcggcccc < 2:552991/144‑6 (MQ=39)
tgtgCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCCTGTGTCGCCGACAGCATAGCAACACTGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggcccc < 2:552992/144‑6 (MQ=255)
tgtgCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGAGAACAGGAGCAACTCTTTTTGTCATGTTTCGCCGACAGAATAGAAACACCGCTAGGGGGGGGGATTGGCTTTGTGTCGCGAAAGGGCCGCATAgcggcccc < 2:552994/144‑6 (MQ=255)
ttCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTcc < 6:118308/143‑1 (MQ=255)
ttCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTTTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt < 1:420510/143‑1 (MQ=255)
gTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt < 1:131884/144‑1 (MQ=255)
gTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt < 1:420509/144‑1 (MQ=255)
gTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt < 1:420508/144‑1 (MQ=255)
gTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgtgt < 1:420507/144‑1 (MQ=255)
gCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGTGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGc < 1:391310/144‑1 (MQ=38)
gCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGc < 1:391311/144‑1 (MQ=255)
gCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAACAGAGCAACACCGCTCAGGGGGGGGAGTGGCTTTGTTTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGc < 1:73400/144‑1 (MQ=255)
gCCGGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCTCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATg < 5:61838/143‑1 (MQ=255)
ccTGGGCAGCGATTAGTCGGGCGGACACGAGCAATTCCTTTTGTTATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGca < 1:629497/144‑1 (MQ=37)
ccTGGGCAGCAATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGca < 1:629499/144‑1 (MQ=38)
tAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg < 3:33602/94‑1 (MQ=21)
|||
CTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGG > AE015451_phaM1/5555469‑5555643
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAT > AE015451_phaM1/5555486‑5555650
|
TTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTTTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAAC < LH00444:58:22357VLT4:2:2240:11059:6897/151‑1 (MQ=60)
GTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAAC < LH00444:58:22357VLT4:2:1274:24904:28007/151‑1 (MQ=60)
GTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAAC < LH00444:58:22357VLT4:2:2240:11042:6897/151‑1 (MQ=60)
GTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAAC < LH00444:58:22357VLT4:2:2240:11051:6883/151‑1 (MQ=60)
GTCGGCCTGGGCAGCGATTAGNCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGNCGCNAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAAC < LH00444:58:22357VLT4:2:2240:11067:6883/151‑1 (MQ=60)
TCCTGGGCAGCGATTGGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAACAGAGCAACACCGCTCAGGGGGGGGAGTGGCTTTGTTTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAC < LH00444:58:22357VLT4:2:1194:4358:5468/151‑1 (MQ=60)
GCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGTGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAC < LH00444:58:22357VLT4:2:2201:39883:28805/151‑1 (MQ=60)
GCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAC < LH00444:58:22357VLT4:2:2201:39899:28805/151‑1 (MQ=60)
GCCGGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCTCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAAC < LH00444:90:22JGJLLT3:8:2109:46630:10149/151‑1 (MQ=60)
CCTGGGCAGCGATTAGTCGGGCGGACACGAGCAATTCCTTTTGTTATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACC < LH00444:58:22357VLT4:2:2481:1469:13019/151‑1 (MQ=60)
CCTGGGCAGCAATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACC < LH00444:58:22357VLT4:2:2481:1461:13033/151‑1 (MQ=60)
TAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAT < LH00444:62:22GH52LT3:8:1155:20232:10197/101‑1 (MQ=60)
|
GTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAT > AE015451_phaM1/5555486‑5555650
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
