BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089662.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,576,523 number of mapped reads = 11,366,139 (83.72%) number of supplementary alignments = 383 (0%) number of secondary alignments = 0 number of mapped bases = 538,657,689 bp number of sequenced bases = 538,548,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,346,780 duplication rate = 19.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3509 >>>>>>> ACTG content number of A's = 161,704,639 bp (30.03%) number of C's = 103,443,562 bp (19.21%) number of T's = 156,265,992 bp (29.02%) number of G's = 117,133,726 bp (21.75%) number of N's = 320 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,565,323 number of insertions = 20,989 mapped reads with insertion percentage = 0.18% number of deletions = 73,832 mapped reads with deletion percentage = 0.65% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.174X std coverageData = 1.3305X There is a 6.47% of reference with a coverageData >= 1X There is a 2.95% of reference with a coverageData >= 2X There is a 1.78% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.86% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 45462476 0.182396640849292 1.3510612712765016 chr2 243199373 51913477 0.21346057088724485 1.6626383962430897 chr3 198022430 51071774 0.25790903586023056 1.6518485662070965 chr4 191154276 23860282 0.12482212011830696 0.9853849510701962 chr5 180915260 22859429 0.12635434401719348 0.9959755769795716 chr6 171115067 34654960 0.20252430488777473 1.3844791210453773 chr7 159138663 35823813 0.22511068224822273 1.617054605985163 chr8 146364022 43395480 0.2964900759559614 1.8958493314523719 chr9 141213431 18662448 0.13215774071801994 1.1226189287668331 chr10 135534747 21520775 0.15878418985797052 1.1961726975474665 chr11 135006516 25260244 0.18710388763754188 1.3122527881484092 chr12 133851895 18601960 0.13897419980494113 1.0525346690880935 chr13 115169878 15460026 0.13423671422140432 1.0322669586749311 chr14 107349540 17839818 0.16618439166111004 1.251448367312029 chr15 102531392 13348113 0.13018562158992242 1.0276112816647065 chr16 90354753 10309176 0.11409666517488018 0.9171138734976932 chr17 81195210 12328201 0.15183409218351673 1.1238357990476466 chr18 78077248 26103001 0.3343227594292258 1.9051400220873276 chr19 59128983 8190040 0.13851143017291537 1.5223682077096292 chr20 63025520 12104459 0.19205647172764304 1.2881105711494107 chr21 48129895 8490644 0.1764110227125989 1.287034368370335 chr22 51304566 4058692 0.07910976188747021 0.7433881988185583 chrMT 16571 579768 34.9869048337457 51.764086043420534 chrX 155270560 15788118 0.10168133611419963 0.9145540672218897 chrY 59373566 970515 0.016345910569023257 0.3612437444753184