BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081943.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 = 3,386,896 number of mapped reads = 3,108,136 (91.77%) number of supplementary alignments = 20,072 (0.59%) number of secondary alignments = 0 number of mapped bases = 212,272,323 bp number of sequenced bases = 212,185,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 166,124 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0119 >>>>>>> ACTG content number of A's = 60,218,648 bp (28.38%) number of C's = 39,473,522 bp (18.6%) number of T's = 66,427,991 bp (31.31%) number of G's = 46,038,019 bp (21.7%) number of N's = 27,004 bp (0.01%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,704,527 number of insertions = 15,996 mapped reads with insertion percentage = 0.51% number of deletions = 49,517 mapped reads with deletion percentage = 1.58% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.0686X std coverageData = 0.7705X There is a 5.75% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 18612505 0.07467385607837664 1.5647420220790673 chr2 243199373 18761193 0.0771432622073413 1.0405016436499854 chr3 198022430 12480336 0.06302486036556566 0.2957257418249955 chr4 191154276 11381505 0.059540938545366365 0.31888219948916857 chr5 180915260 10882679 0.06015346079706046 0.2905697712466732 chr6 171115067 18660508 0.10905239571919169 0.55656759171292 chr7 159138663 14147764 0.0889021167659301 1.051876729319434 chr8 146364022 12127652 0.08285951584467938 0.9277640158375611 chr9 141213431 10718689 0.07590417514889218 0.8182449612377098 chr10 135534747 8839823 0.06522182094013132 0.7585907958340357 chr11 135006516 9586289 0.07100612091937844 0.4969732817601518 chr12 133851895 8757720 0.0654284349130806 0.3298963709862518 chr13 115169878 5580517 0.04845465756245743 0.24822962561832987 chr14 107349540 5274639 0.04913518027184839 0.3499417332511428 chr15 102531392 4893939 0.04773112804320456 0.2543136888051079 chr16 90354753 4666358 0.05164485370238354 0.3935596918399906 chr17 81195210 5629718 0.06933559257990711 0.3514180627780111 chr18 78077248 6295576 0.08063265754448723 1.4000285897731541 chr19 59128983 4702591 0.07953106516308593 1.2098511966314343 chr20 63025520 5279213 0.08376310104224448 0.34742318884511897 chr21 48129895 2298574 0.04775771898110312 0.3338811967010262 chr22 51304566 1730190 0.03372389896057205 0.2055939651197487 chrMT 16571 6953 0.4195884376320077 0.7067696652185939 chrX 155270560 10448560 0.06729260202320389 0.4159309060672314 chrY 59373566 508832 0.008570009084514142 0.22733499909538157