BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006102.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 10,914,922 number of mapped reads = 9,717,537 (89.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,924,052 number of mapped paired reads (second in pair) = 4,793,485 number of mapped paired reads (both in pair) = 8,993,152 number of mapped paired reads (singletons) = 724,385 number of mapped bases = 375,739,968 bp number of sequenced bases = 375,701,072 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 611,084 duplication rate = 5.56% >>>>>>> Insert size mean insert size = 54,005.2977 std insert size = 2,233,237.9827 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 47.5626 >>>>>>> ACTG content number of A's = 103,158,296 bp (27.46%) number of C's = 81,630,788 bp (21.73%) number of T's = 105,737,879 bp (28.14%) number of G's = 85,158,788 bp (22.67%) number of N's = 15,321 bp (0%) GC percentage = 44.39% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,836,898 number of insertions = 11,270 mapped reads with insertion percentage = 0.12% number of deletions = 30,265 mapped reads with deletion percentage = 0.31% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 0.1214X std coverageData = 0.6579X There is a 7.05% of reference with a coverageData >= 1X There is a 2.83% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 31218020 0.12524751141943996 0.7188190216652957 chr2 243199373 32467140 0.13350009746941247 0.6925102368368612 chr3 198022430 26058109 0.13159170403069995 0.5580585284050192 chr4 191154276 23965207 0.12537102230451805 0.5700121523279198 chr5 180915260 23186737 0.12816352252430227 0.5561776855945615 chr6 171115067 21503400 0.12566631552088864 0.6004265931092986 chr7 159138663 20823386 0.13085057777568485 0.9428411863967144 chr8 146364022 19302521 0.13188023078513106 0.7759194655742008 chr9 141213431 16029589 0.11351320399544715 0.6148128016383749 chr10 135534747 17962691 0.13253199934036103 0.594133404972702 chr11 135006516 17931016 0.13281593015851176 1.0023943707633334 chr12 133851895 17290993 0.12918003887804502 0.5597855784767296 chr13 115169878 12240183 0.10627937801583848 0.5078510223547109 chr14 107349540 11712366 0.10910494819074214 0.5356796429453724 chr15 102531392 11548317 0.11263201225240363 0.5280433255831583 chr16 90354753 11401661 0.1261877280545496 0.5970057741420051 chr17 81195210 10871387 0.1338919746620521 0.6591798117354739 chr18 78077248 10123679 0.12966234414409689 0.8923979826496957 chr19 59128983 7543285 0.12757339323762765 0.7540526758812873 chr20 63025520 8560124 0.1358199662612859 0.5868845213141786 chr21 48129895 5120858 0.10639661690514804 0.5644262593479514 chr22 51304566 4821220 0.09397253258121314 0.5227825371869971 chrMT 16571 9612 0.5800494840383803 1.1966381321377706 chrX 155270560 11460658 0.07381088855479107 0.45545782749299285 chrY 59373566 2587809 0.043585204230448274 0.36519140513842047