BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090130.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 18,568,594 number of mapped reads = 15,118,093 (81.42%) number of supplementary alignments = 747 (0%) number of secondary alignments = 0 number of mapped bases = 710,045,218 bp number of sequenced bases = 709,911,127 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,587,421 duplication rate = 11.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0324 >>>>>>> ACTG content number of A's = 208,432,199 bp (29.36%) number of C's = 146,772,730 bp (20.67%) number of T's = 202,627,807 bp (28.54%) number of G's = 152,042,146 bp (21.42%) number of N's = 36,245 bp (0.01%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 3,472,615 number of insertions = 27,482 mapped reads with insertion percentage = 0.18% number of deletions = 87,509 mapped reads with deletion percentage = 0.58% homopolymer indels = 46.04% >>>>>>> Coverage mean coverageData = 0.2294X std coverageData = 1.5769X There is a 11.9% of reference with a coverageData >= 1X There is a 4.91% of reference with a coverageData >= 2X There is a 2.42% of reference with a coverageData >= 3X There is a 1.3% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 58037980 0.23284989127469416 2.8289191503294373 chr2 243199373 73989371 0.30423339537145927 2.025778471521442 chr3 198022430 64252090 0.32446874831300676 1.0280281708772514 chr4 191154276 35934890 0.18798894145585318 0.8094319789564579 chr5 180915260 32163143 0.1777801551953108 0.7406809885221712 chr6 171115067 38675874 0.22602260968638138 0.9507630856688193 chr7 159138663 51984696 0.3266628927251953 3.118988350913048 chr8 146364022 62400263 0.42633607731823603 2.2676485999706397 chr9 141213431 21954608 0.15547110387821397 1.0843007085656882 chr10 135534747 22153945 0.163455833211538 1.1675547257003063 chr11 135006516 29992586 0.2221565809460634 1.1547767112331333 chr12 133851895 25668898 0.19177089722935936 0.8092661092416515 chr13 115169878 21193015 0.18401525961501844 0.740360248990067 chr14 107349540 25057663 0.23342124241985573 0.8999619757482487 chr15 102531392 18955190 0.18487206337742884 0.7550251744664359 chr16 90354753 14870038 0.16457394333201264 0.7751142172906339 chr17 81195210 14510117 0.17870656409411342 0.820527407860896 chr18 78077248 26009639 0.3331269949473629 1.8370178771609063 chr19 59128983 12767219 0.21592150502571641 1.6960784683561232 chr20 63025520 17561445 0.27864022383313936 0.9933381235865412 chr21 48129895 10268073 0.21334085603137093 0.9712502226461017 chr22 51304566 6201164 0.12086963175948122 0.6036402158086042 chrMT 16571 910824 54.96493874841591 35.507525207691565 chrX 155270560 22508875 0.14496550408525608 0.9000577263642082 chrY 59373566 2023612 0.034082709467037904 1.3272852931675203