BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549031.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 = 8,810,048 number of mapped reads = 7,637,018 (86.69%) number of secondary alignments = 0 number of mapped bases = 302,254,312 bp number of sequenced bases = 302,222,092 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,848 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4448 >>>>>>> ACTG content number of A's = 87,813,741 bp (29.06%) number of C's = 62,377,419 bp (20.64%) number of T's = 88,778,315 bp (29.38%) number of G's = 63,249,591 bp (20.93%) number of N's = 3,026 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 793,150 number of insertions = 9,514 mapped reads with insertion percentage = 0.12% number of deletions = 24,500 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0976X std coverageData = 1.3135X There is a 6.29% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% 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 0.01% 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 22917707 0.09194643892181115 0.8316519803163942 chr2 243199373 27258403 0.11208253814042522 0.5968480931941919 chr3 198022430 20398947 0.1030133152087872 0.4619034680996988 chr4 191154276 19639867 0.1027435399875648 0.4717904994805675 chr5 180915260 18522771 0.10238368504680036 0.46436491743062086 chr6 171115067 18376280 0.10739136139309112 0.5030236346170754 chr7 159138663 17231064 0.10827704390101606 0.7656803210643454 chr8 146364022 16805329 0.11481871549006764 5.453979197903564 chr9 141213431 12716908 0.09005452179686789 0.5478882314897543 chr10 135534747 14737475 0.10873576943335424 0.5359708996842192 chr11 135006516 14374306 0.10647120173073721 0.798714468823511 chr12 133851895 14535181 0.10859152199526201 0.48355226451268374 chr13 115169878 8805285 0.07645475668559795 0.3990703364251221 chr14 107349540 8733667 0.08135728387844046 0.46009731597849723 chr15 102531392 8168343 0.07966675220794818 0.40352931461728886 chr16 90354753 8082883 0.08945719767503542 0.4496574938267889 chr17 81195210 8676550 0.10686036774829451 0.5165412312039103 chr18 78077248 7961696 0.10197203671932699 0.9037551381281255 chr19 59128983 6133114 0.10372432754339779 0.7702052386105462 chr20 63025520 6432476 0.10206145066315994 0.4728739363340565 chr21 48129895 3484664 0.07240123835715827 0.41316499480399216 chr22 51304566 3495850 0.06813915938787983 0.42132577717655056 chrMT 16571 62721 3.784985818598757 4.646625585697383 chrX 155270560 13936032 0.08975321529078018 0.49027198732672556 chrY 59373566 766793 0.012914720331940311 0.1875663456029478