BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081051.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 = 1,651,773 number of mapped reads = 1,163,717 (70.45%) number of supplementary alignments = 4,999 (0.3%) number of secondary alignments = 0 number of mapped bases = 71,808,385 bp number of sequenced bases = 71,785,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,408 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8981 >>>>>>> ACTG content number of A's = 20,359,616 bp (28.36%) number of C's = 13,651,700 bp (19.02%) number of T's = 21,794,781 bp (30.36%) number of G's = 15,978,497 bp (22.26%) number of N's = 953 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 520,317 number of insertions = 4,614 mapped reads with insertion percentage = 0.39% number of deletions = 13,328 mapped reads with deletion percentage = 1.13% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.1954X There is a 2.06% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 5102621 0.020471848694009875 0.22977741765481832 chr2 243199373 5956638 0.024492818079757138 0.20104499344362714 chr3 198022430 4630303 0.023382719826233828 0.1686992428390592 chr4 191154276 4366439 0.022842486662448504 0.16948592419564604 chr5 180915260 4226716 0.02336296009524017 0.16911205738045146 chr6 171115067 4953934 0.028950893026854264 0.2138364887058741 chr7 159138663 4367989 0.027447691954028797 0.27847659639798045 chr8 146364022 4152089 0.028368235193755472 0.23143386205529046 chr9 141213431 2982409 0.02111986784033312 0.18129424533792596 chr10 135534747 3478262 0.02566324929208006 0.1891025396883157 chr11 135006516 3742622 0.02772178788763055 0.20640165972197655 chr12 133851895 3662823 0.027364745190944065 0.18356360437740438 chr13 115169878 2654450 0.02304812721951481 0.16745163186403236 chr14 107349540 2280235 0.021241218173827292 0.16366257492030037 chr15 102531392 2135327 0.020826080270128392 0.16441383302190618 chr16 90354753 2065270 0.022857347637262646 0.17166712765388323 chr17 81195210 1688318 0.020793320197090445 0.16778142379449384 chr18 78077248 1897690 0.024305288014249683 0.289749802180048 chr19 59128983 1417960 0.023980794663760747 0.2160915432507029 chr20 63025520 1469354 0.023313635492416405 0.1697956357813006 chr21 48129895 796887 0.01655700682496814 0.1472499661479192 chr22 51304566 806306 0.015716067065063954 0.1370209578861254 chrMT 16571 30188 1.821736769054372 1.6120029042511221 chrX 155270560 2794397 0.017996953189323206 0.15560346596073973 chrY 59373566 149158 0.002512195410327889 0.06331323125049304