BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038445.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,695,706 number of mapped reads = 11,941,488 (94.06%) number of supplementary alignments = 182,467 (1.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,042,763 number of mapped paired reads (second in pair) = 5,898,725 number of mapped paired reads (both in pair) = 11,777,730 number of mapped paired reads (singletons) = 163,758 number of mapped bases = 1,696,683,680 bp number of sequenced bases = 1,695,489,931 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,663,057 duplication rate = 9.31% >>>>>>> Insert size mean insert size = 72,580.4144 std insert size = 2,528,106.7078 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 53.7653 >>>>>>> ACTG content number of A's = 493,295,396 bp (29.09%) number of C's = 344,500,258 bp (20.32%) number of T's = 495,261,981 bp (29.21%) number of G's = 362,396,274 bp (21.37%) number of N's = 36,022 bp (0%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 22,407,985 number of insertions = 293,053 mapped reads with insertion percentage = 2.31% number of deletions = 595,627 mapped reads with deletion percentage = 4.79% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.5481X std coverageData = 6.6161X There is a 23.29% of reference with a coverageData >= 1X There is a 12.25% of reference with a coverageData >= 2X There is a 6.36% of reference with a coverageData >= 3X There is a 3.69% of reference with a coverageData >= 4X There is a 2.13% of reference with a coverageData >= 5X There is a 1.3% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 102159174 0.4098652737158075 4.030871696896107 chr2 243199373 171575681 0.7054939282265337 7.997122661811193 chr3 198022430 115500997 0.5832722939517508 1.3784269702377498 chr4 191154276 99061647 0.5182287787273981 6.233331435449919 chr5 180915260 95127617 0.5258131182521585 1.3474007878604461 chr6 171115067 122053070 0.7132806721222276 7.7965720559806035 chr7 159138663 119816352 0.752905357763374 6.507600583861714 chr8 146364022 75765570 0.5176515988334893 1.8641495095649012 chr9 141213431 68132559 0.4824793117589502 8.967306985532966 chr10 135534747 72097403 0.5319477447358942 17.52189515742495 chr11 135006516 97149273 0.7195895122573195 3.7414763851624726 chr12 133851895 57955678 0.4329836196939909 1.1586720411574742 chr13 115169878 87427846 0.7591207659349956 1.668654519440582 chr14 107349540 31182514 0.2904764566294369 0.9769239526040753 chr15 102531392 30157448 0.29412892394945733 0.9057844913846328 chr16 90354753 67592550 0.7480796278641811 14.099175954040033 chr17 81195210 35940339 0.4426411237805777 3.492106335248066 chr18 78077248 25780798 0.3301960386718548 7.11156575038492 chr19 59128983 18511682 0.3130728969243391 2.5262218355633497 chr20 63025520 63321149 1.0046906237346396 2.7144324776014233 chr21 48129895 14383158 0.29884041924462956 3.1122177338356942 chr22 51304566 9698772 0.18904305710333852 0.8400808237925995 chrMT 16571 3984845 240.4710035604369 112.21651209848069 chrX 155270560 87514715 0.5636272259209988 1.6325708291284144 chrY 59373566 24792843 0.4175737566444973 12.088009357962902