BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1006434.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 1,249,204
number of mapped reads = 1,050,869 (84.12%)
number of supplementary alignments = 2,473 (0.2%)
number of secondary alignments = 0
number of mapped bases = 58,137,434 bp
number of sequenced bases = 58,119,673 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 70,035
duplication rate = 5.96%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.4362
>>>>>>> ACTG content
number of A's = 16,233,523 bp (27.93%)
number of C's = 12,592,878 bp (21.67%)
number of T's = 16,581,582 bp (28.53%)
number of G's = 12,709,049 bp (21.87%)
number of N's = 2,641 bp (0%)
GC percentage = 43.53%
>>>>>>> Mismatches and indels
general error rate = 0.0044
number of mismatches = 246,367
number of insertions = 4,684
mapped reads with insertion percentage = 0.44%
number of deletions = 10,982
mapped reads with deletion percentage = 1.04%
homopolymer indels = 41.93%
>>>>>>> Coverage
mean coverageData = 0.0188X
std coverageData = 0.2481X
There is a 1.65% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 4663577 0.018710392701488998 0.20216007025940025
chr2 243199373 4820181 0.019819874288902875 0.17175837446387288
chr3 198022430 3785846 0.019118268571898647 0.1534340057144613
chr4 191154276 3616587 0.01891972848151197 0.15632634596422004
chr5 180915260 3450814 0.01907420081644854 0.1528414592309895
chr6 171115067 3254643 0.019020201184270932 0.18432075031313902
chr7 159138663 4491831 0.028225893791755684 0.21904439895967054
chr8 146364022 2910114 0.019882714072998076 0.38437516512129755
chr9 141213431 2397391 0.016977074935598725 0.1574274245038895
chr10 135534747 2744324 0.020248121317554088 0.181134051109767
chr11 135006516 2634780 0.019515946919184256 0.16508581440503448
chr12 133851895 2585348 0.019314989899844152 0.1545418470231685
chr13 115169878 1795735 0.01559205437380076 0.13841100269080742
chr14 107349540 1935489 0.01802978382580866 0.8960998155717961
chr15 102531392 1691476 0.016497152403821845 0.14243736517782288
chr16 90354753 1713594 0.018965178290067376 0.16270158707655208
chr17 81195210 1578847 0.01944507563931419 0.1623588480412414
chr18 78077248 1514093 0.01939224343562929 0.19095625571974686
chr19 59128983 1176440 0.019896164965326733 0.19225980846473742
chr20 63025520 1262341 0.020029045377174197 0.22324406150114937
chr21 48129895 1071065 0.022253632591552507 0.1740887954379082
chr22 51304566 746650 0.014553285569163571 0.15020617747778073
chrMT 16571 79314 4.786313439140668 4.463889788662075
chrX 155270560 1721332 0.011086016563603557 0.11828192092046157
chrY 59373566 495622 0.008347519500513073 0.1323415978003033