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 |
|
A0 F0 I1 R1
|
52 |
69.5 |
2964196 |
98.4% |
2916768 |
145.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,684,230 |
+CGGG |
intergenic (‑133/+71) |
PP_4986 ← / ← PP_4987 |
hemolysin III family channel protein/putative Chemotaxis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,684,230 | 1 | . | C | 100.0%
| 36.3
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (1/12); total (1/12) |
| * | NC_002947_CJ‑RC | 5,684,230 | 2 | . | G | 100.0%
| 38.6
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/12); total (1/12) |
| * | NC_002947_CJ‑RC | 5,684,230 | 3 | . | G | 100.0%
| 37.7
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/12); total (1/12) |
| * | NC_002947_CJ‑RC | 5,684,230 | 4 | . | G | 100.0%
| 38.2
/ NA
| 13 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/12); total (1/12) |
ACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATG > NC_002947_CJ‑RC/5684086‑5684350
||||
aCCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccgg < 8:293182/148‑4 (MQ=255)
gTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccggggct < 6:144515/149‑8 (MQ=255)
aaaCACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGcc < 1:128759/149‑1 (MQ=38)
aaaCACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGcc < 7:74241/149‑1 (MQ=38)
cacaGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTa < 1:112103/149‑1 (MQ=37)
caGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATc < 3:104176/149‑1 (MQ=37)
gACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATcgc < 1:222294/149‑1 (MQ=37)
aGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACaa < 6:286943/147‑1 (MQ=37)
aGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAgg < 8:226327/149‑1 (MQ=25)
gggggCGGGGTTCCTGTTGTGATGCTGATGGCTTGGTTCTTTGTGGGCGCGGCCTTGTGGGGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTCCCACTCCATGACCCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGcc < 2:141963/147‑1 (MQ=21)
gTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGc < 5:10860/148‑1 (MQ=25)
tgtCGCTAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTg < 3:92530/148‑1 (MQ=37)
ccccAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGac < 3:68332/83‑1 (MQ=21)
cAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTa < 7:86245/106‑1 (MQ=37)
tttCATTGCCACTGCATGAACCGCCGGGGGTGCTGGGCAGCCCAATAGCCACACAACGCCGCGCCCCCACCAGACCCCCCCGCCCAGCGCCGCCCAAACAAAACAAGGTAACGTTGGAGATCCGCGGCACGCACCCGCCATTGCaaat > 8:156360/1‑146 (MQ=255)
||||
ACCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATG > NC_002947_CJ‑RC/5684086‑5684350
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTT > NC_002947_CJ‑RC/5684093‑5684344
|
AACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCG < NB501016:282:H2V7GAFX2:1:11202:4905:15601/151‑1 (MQ=60)
CAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCC < NB501016:282:H2V7GAFX2:4:11502:6159:7927/151‑1 (MQ=60)
CAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCC < NB501016:282:H2V7GAFX2:1:11301:16500:3430/151‑1 (MQ=60)
ACACTGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTAT < NB501016:282:H2V7GAFX2:1:11209:3630:18340/151‑1 (MQ=60)
ACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCG < NB501016:282:H2V7GAFX2:2:11209:4642:7701/151‑1 (MQ=60)
AGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCG < NB501016:282:H2V7GAFX2:1:21107:18995:7851/151‑1 (MQ=60)
acctgaccttggttaggatgtgaggcgcagggcctggtgggctggaGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGG < NB501016:282:H2V7GAFX2:3:11508:4448:16099/105‑1 (MQ=60)
GGGGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCC < NB501016:282:H2V7GAFX2:3:11403:7172:3032/150‑1 (MQ=60)
GCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcgggggggggggggcgcccacaagcgccacaaaaccgcggccccaccccccccccccccccagcgccgcccaaacaaaacaaag > NB501016:282:H2V7GAFX2:2:21301:25103:7981/1‑65 (MQ=60)
CTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcggggggggggggggggcccgtgccgagaccaagccggggccccacccaccccccccgcccgggggcgccccggcaaaacaccctgcgggg > NB501016:282:H2V7GAFX2:1:11204:10071:3509/1‑60 (MQ=60)
GTGTCGCTAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGC < NB501016:282:H2V7GAFX2:2:11207:15059:3577/150‑1 (MQ=60)
GTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcggggggggggggcggcccgataggggccccaggccgcgggcccgcccgcccccccccccccggggcgcccctccggaccaaggggggggtggg > NB501016:282:H2V7GAFX2:3:21508:18888:4630/1‑57 (MQ=60)
CGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcgggggggggggggcgcccgatagcgacacaaagccgcgcccccccccccccaccccgccccgcgccgcgccaacaaaacaaccgaagggtggggatg > NB501016:282:H2V7GAFX2:2:11105:6925:7000/1‑53 (MQ=60)
CGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCcgggggggctgggccgcccgatagcggcacaacgccgcgcccccaccccgcccccacgcccggcgccgcccaaactaaccaagggcagggtggagctg > NB501016:282:H2V7GAFX2:4:11507:21736:11679/1‑53 (MQ=60)
GCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACC < NB501016:282:H2V7GAFX2:2:11202:18503:10364/85‑1 (MQ=60)
CCCCAGGCTTTCATTGCCACTGCATGAACCGCcggggcggcggcgccgcccgataaccccacaaagccgcgaccaccccacaccacacagccccgcgccccacaaccaaaacaaccacagcttgcagaaaacccgaaccccccacccgat > NB501016:282:H2V7GAFX2:1:11210:8495:19964/1‑32 (MQ=60)
CCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAA < NB501016:282:H2V7GAFX2:4:11504:11818:12239/108‑1 (MQ=60)
|
TACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTT > NC_002947_CJ‑RC/5684093‑5684344
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
