BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085059.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 = 1,409,804 number of mapped reads = 1,137,399 (80.68%) number of supplementary alignments = 7,368 (0.52%) number of secondary alignments = 0 number of mapped bases = 71,689,439 bp number of sequenced bases = 71,666,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,618 duplication rate = 1.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0173 >>>>>>> ACTG content number of A's = 21,764,832 bp (30.37%) number of C's = 13,560,863 bp (18.92%) number of T's = 20,824,034 bp (29.06%) number of G's = 15,515,342 bp (21.65%) number of N's = 1,570 bp (0%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 652,455 number of insertions = 5,517 mapped reads with insertion percentage = 0.48% number of deletions = 14,363 mapped reads with deletion percentage = 1.25% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2054X There is a 2.13% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 5623281 0.022560750209725654 0.3013459529855817 chr2 243199373 6204370 0.02551145557435298 0.21790376684629564 chr3 198022430 4954488 0.025019832349294977 0.16861123577415094 chr4 191154276 4880975 0.025534218235327366 0.17417848184343634 chr5 180915260 4526886 0.02502213467233223 0.16833910832414434 chr6 171115067 4261188 0.024902471037223158 0.18815037228465453 chr7 159138663 3957166 0.02486615084858417 0.19871044504833194 chr8 146364022 3746432 0.025596672931002127 0.29423977239594934 chr9 141213431 3011445 0.02132548567565078 0.19605002212524336 chr10 135534747 3372299 0.024881435016807903 0.22206375779421575 chr11 135006516 3239752 0.023997004707535748 0.20206309122305835 chr12 133851895 3215286 0.024021221365599643 0.16562797423126227 chr13 115169878 2335976 0.020282872922727242 0.15083730171261336 chr14 107349540 2172097 0.02023387338222409 0.15679502771795384 chr15 102531392 1971229 0.019225614336729185 0.1467519852724172 chr16 90354753 1898913 0.02101619380222311 0.16311412539268424 chr17 81195210 1714823 0.02111975570972721 0.16287793721045607 chr18 78077248 1944161 0.02490048061120187 0.3419616228267482 chr19 59128983 1186387 0.020064390419162123 0.22225477530901655 chr20 63025520 1398127 0.022183505982973247 0.1608543234310012 chr21 48129895 921847 0.019153314171992272 0.15467994078168565 chr22 51304566 702182 0.013686540102493022 0.12417129392726081 chrMT 16571 2315 0.1397018888419528 0.39188478513124936 chrX 155270560 4262953 0.027454998552204617 0.18853506769002987 chrY 59373566 184861 0.003113523617564086 0.07412217588476747