BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548943.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,913,772 number of mapped reads = 6,920,943 (87.45%) number of secondary alignments = 0 number of mapped bases = 273,592,400 bp number of sequenced bases = 273,564,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 255,654 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.606 >>>>>>> ACTG content number of A's = 79,080,623 bp (28.91%) number of C's = 57,601,943 bp (21.06%) number of T's = 79,467,498 bp (29.05%) number of G's = 57,411,599 bp (20.99%) number of N's = 2,399 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 854,763 number of insertions = 9,777 mapped reads with insertion percentage = 0.14% number of deletions = 21,780 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.49% >>>>>>> Coverage mean coverageData = 0.0884X std coverageData = 0.9254X There is a 7.27% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 21494492 0.08623646317815994 0.9639120210148423 chr2 243199373 23040550 0.09473934786830228 0.6133702466858268 chr3 198022430 18315725 0.09249318372671217 0.35450951855554047 chr4 191154276 17950909 0.0939079646850275 0.3825716682687047 chr5 180915260 16894167 0.09338165835209257 0.36600810223565344 chr6 171115067 15893632 0.0928827149978558 0.39894073168183464 chr7 159138663 15258229 0.09588008792055769 0.8756898599786196 chr8 146364022 14220145 0.09715601420135886 3.366802558096014 chr9 141213431 11407060 0.08077886019213003 0.6173721618149616 chr10 135534747 12542423 0.09254027677492917 0.5268469766486693 chr11 135006516 12404842 0.09188328361869585 0.6049806603754319 chr12 133851895 12473820 0.09319120958280046 0.37608752592585776 chr13 115169878 8761280 0.07607266893171494 0.31807449063288995 chr14 107349540 8330050 0.0775974447584964 0.4247740841892473 chr15 102531392 7802243 0.07609613843924015 0.323832207532363 chr16 90354753 7586659 0.08396524530369753 0.3979957999374101 chr17 81195210 7281036 0.08967322087103415 0.38078201291435815 chr18 78077248 7327025 0.09384327941476626 1.1224410749726499 chr19 59128983 5638918 0.09536639586715029 0.9665745530857721 chr20 63025520 5498427 0.08724127940554874 0.37149788889225815 chr21 48129895 3481985 0.07234557648629818 0.3806698496614599 chr22 51304566 3019966 0.05886349374829523 0.3305337497107641 chrMT 16571 11052 0.6669482831452538 1.0372118533140553 chrX 155270560 15986758 0.10296065139457215 0.48445409614497564 chrY 59373566 971007 0.016354197084945177 0.22582787129090207