BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082743.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,912,446 number of mapped reads = 3,403,369 (86.99%) number of supplementary alignments = 27,835 (0.71%) number of secondary alignments = 0 number of mapped bases = 232,041,139 bp number of sequenced bases = 231,953,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,235 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4035 >>>>>>> ACTG content number of A's = 66,753,557 bp (28.78%) number of C's = 41,870,646 bp (18.05%) number of T's = 75,571,520 bp (32.58%) number of G's = 47,744,556 bp (20.58%) number of N's = 12,985 bp (0.01%) GC percentage = 38.64% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,014,987 number of insertions = 18,373 mapped reads with insertion percentage = 0.54% number of deletions = 51,835 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.075X std coverageData = 0.537X There is a 5.82% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 21521237 0.08634376481653781 0.8771820452568256 chr2 243199373 23570050 0.09691657387619992 0.666926073550901 chr3 198022430 16771736 0.08469614275514142 0.35296128762434703 chr4 191154276 15553816 0.08136786853776684 0.3580238376909016 chr5 180915260 11719499 0.0647789412568072 0.3099178725309865 chr6 171115067 16755095 0.09791712263420965 0.5455561237592441 chr7 159138663 15685620 0.09856573948971785 0.5156228985025397 chr8 146364022 18019575 0.12311478431495959 0.9430615519613936 chr9 141213431 6985821 0.049469947373490274 0.48833479868250523 chr10 135534747 7711311 0.05689545427048313 0.38797286191997216 chr11 135006516 9429521 0.06984493252162732 0.442488978057185 chr12 133851895 7049501 0.052666426575432496 0.2948821806928844 chr13 115169878 5517435 0.04790692753881358 0.2638233934204498 chr14 107349540 4835293 0.04504251252497216 0.2949904993581327 chr15 102531392 4528975 0.04417159380807002 0.2545919305646777 chr16 90354753 8721055 0.09652015760587603 0.43703439063621646 chr17 81195210 5153042 0.0634648521753931 0.3600505937484983 chr18 78077248 7857206 0.10063374672222054 1.0838305996893316 chr19 59128983 2783957 0.04708278172144446 0.6058855606940428 chr20 63025520 4247205 0.06738865462752232 0.33480970381827385 chr21 48129895 4744225 0.09857127259471478 0.3940105942387905 chr22 51304566 2851438 0.055578639920665154 0.2826832786487695 chrMT 16571 260355 15.711483917687527 9.023792797159585 chrX 155270560 9409143 0.06059837099833993 0.3495622625767377 chrY 59373566 359028 0.0060469334114107275 0.11921740332226714