BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046450.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 8,101,054 number of mapped reads = 8,064,731 (99.55%) number of supplementary alignments = 37,066 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,038,391 number of mapped paired reads (second in pair) = 4,026,340 number of mapped paired reads (both in pair) = 8,039,256 number of mapped paired reads (singletons) = 25,475 number of mapped bases = 786,639,652 bp number of sequenced bases = 786,399,295 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,615,396 duplication rate = 39.12% >>>>>>> Insert size mean insert size = 18,705.7165 std insert size = 1,386,343.1035 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 53.5069 >>>>>>> ACTG content number of A's = 230,144,135 bp (29.27%) number of C's = 163,553,693 bp (20.8%) number of T's = 230,919,738 bp (29.36%) number of G's = 161,708,382 bp (20.56%) number of N's = 73,347 bp (0.01%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 2,713,240 number of insertions = 60,873 mapped reads with insertion percentage = 0.74% number of deletions = 85,568 mapped reads with deletion percentage = 1.02% homopolymer indels = 49.47% >>>>>>> Coverage mean coverageData = 0.2541X std coverageData = 17.0613X There is a 2.9% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% 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 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 128759236 0.516585417052983 25.5782294633342 chr2 243199373 75459042 0.3102764660499351 18.959278421929728 chr3 198022430 58218913 0.2940016088076487 17.684818108098025 chr4 191154276 25756112 0.13473992075385224 9.424284297032889 chr5 180915260 59659565 0.3297652447891903 18.396610254328184 chr6 171115067 49895996 0.2915932353285991 14.45155293641754 chr7 159138663 52949550 0.3327258693885093 15.580832934540048 chr8 146364022 87549244 0.5981609606218665 38.94739683610802 chr9 141213431 8580759 0.0607644679350649 3.021553715276244 chr10 135534747 23474118 0.17319630957808924 10.248635099372931 chr11 135006516 13490965 0.09992825087049872 4.875853868669143 chr12 133851895 19024595 0.14213168218500008 9.597164798880465 chr13 115169878 13172005 0.11437022621487886 8.11001614800051 chr14 107349540 30951643 0.288325809314134 15.406408060096721 chr15 102531392 12176664 0.11876035000090508 7.385579810535702 chr16 90354753 45171706 0.49993724181836896 31.291609436649175 chr17 81195210 30966519 0.38138356930168665 16.640593438382183 chr18 78077248 5157368 0.0660546847142973 2.14930251167984 chr19 59128983 5875032 0.09935959832084378 5.843060097482777 chr20 63025520 8226568 0.1305275704190937 11.28363887222181 chr21 48129895 4244446 0.08818731061017274 9.65141507491359 chr22 51304566 7551768 0.14719485201375643 8.299948675022002 chrMT 16571 70177 4.234928489529902 2.6648385647189072 chrX 155270560 20155740 0.12981044185066376 9.808854983665626 chrY 59373566 101921 0.0017166056692636586 0.0935057615815505