BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617412.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,712,316 (92.85%) number of supplementary alignments = 444,475 (1.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,956,286 number of mapped paired reads (second in pair) = 14,756,030 number of mapped paired reads (both in pair) = 29,190,000 number of mapped paired reads (singletons) = 522,316 number of mapped bases = 2,924,081,776 bp number of sequenced bases = 2,923,448,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,342,515 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 47,081.6025 std insert size = 2,062,501.6913 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.8909 >>>>>>> ACTG content number of A's = 874,290,355 bp (29.91%) number of C's = 586,218,344 bp (20.05%) number of T's = 864,027,084 bp (29.56%) number of G's = 597,858,973 bp (20.45%) number of N's = 1,053,874 bp (0.04%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 33,992,181 number of insertions = 235,534 mapped reads with insertion percentage = 0.78% number of deletions = 281,047 mapped reads with deletion percentage = 0.93% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.9446X std coverageData = 2.8823X There is a 29.44% of reference with a coverageData >= 1X There is a 16.89% of reference with a coverageData >= 2X There is a 10.79% of reference with a coverageData >= 3X There is a 7.46% of reference with a coverageData >= 4X There is a 5.41% of reference with a coverageData >= 5X There is a 4.07% of reference with a coverageData >= 6X There is a 3.15% of reference with a coverageData >= 7X There is a 2.49% of reference with a coverageData >= 8X There is a 2% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.35% of reference with a coverageData >= 11X There is a 1.13% of reference with a coverageData >= 12X There is a 0.96% of reference with a coverageData >= 13X There is a 0.81% of reference with a coverageData >= 14X There is a 0.7% of reference with a coverageData >= 15X There is a 0.6% of reference with a coverageData >= 16X There is a 0.53% of reference with a coverageData >= 17X There is a 0.46% of reference with a coverageData >= 18X There is a 0.4% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188020581 0.7543434806527524 2.704856957348167 chr2 243199373 291929736 1.2003720749724136 3.0298676854455615 chr3 198022430 247212455 1.2484063295253978 3.3671442994254033 chr4 191154276 141108283 0.7381905649863674 2.260207323874844 chr5 180915260 187780214 1.0379456879425206 2.845371039223431 chr6 171115067 134495642 0.7859953209146685 2.5663363761229725 chr7 159138663 218743309 1.3745453485429873 3.1939114173326284 chr8 146364022 129575052 0.885293053780662 3.1960949779833574 chr9 141213431 117024900 0.8287094164577022 2.5822808274520854 chr10 135534747 93707683 0.6913923187535076 2.3713115965190283 chr11 135006516 217226220 1.6090054497814017 3.780399302300881 chr12 133851895 138898519 1.0377030448466942 2.7282962317694004 chr13 115169878 127360319 1.1058474768897473 2.738426745279686 chr14 107349540 84854506 0.7904505785492886 2.8443221846040503 chr15 102531392 66926353 0.6527401188506248 2.316273104510352 chr16 90354753 73167442 0.8097796692554735 3.2729860492861174 chr17 81195210 89399291 1.1010414407450884 3.62140401626749 chr18 78077248 41942844 0.5371967516068189 1.979135927814939 chr19 59128983 41218867 0.6971008955117662 2.2990779996822877 chr20 63025520 99100100 1.5723805214141826 4.639214533105122 chr21 48129895 40126654 0.8337158017901348 2.5047881243758527 chr22 51304566 23305328 0.45425446148399345 2.0336447703635976 chrMT 16571 180371 10.884738398406855 5.017288171367114 chrX 155270560 128448561 0.8272563775129039 2.5296203197861247 chrY 59373566 2328546 0.039218564032350696 0.56094246074341