BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549035.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 = 9,771,022 number of mapped reads = 7,525,268 (77.02%) number of secondary alignments = 0 number of mapped bases = 297,641,833 bp number of sequenced bases = 297,614,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 510,421 duplication rate = 5.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4992 >>>>>>> ACTG content number of A's = 83,971,621 bp (28.21%) number of C's = 63,060,505 bp (21.19%) number of T's = 85,934,936 bp (28.87%) number of G's = 64,646,734 bp (21.72%) number of N's = 265 bp (0%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 778,096 number of insertions = 8,454 mapped reads with insertion percentage = 0.11% number of deletions = 21,167 mapped reads with deletion percentage = 0.28% homopolymer indels = 42.12% >>>>>>> Coverage mean coverageData = 0.0961X std coverageData = 0.6277X There is a 6.03% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 24429283 0.09801092130478584 0.7433142528304316 chr2 243199373 25416575 0.10450921269439292 0.6204900527946564 chr3 198022430 20122285 0.10161619065072577 0.4908680437041545 chr4 191154276 19643553 0.10276282284158791 0.508520013760767 chr5 180915260 18763680 0.10371529742709376 0.48588011360784056 chr6 171115067 18160087 0.10612792501784779 0.5271332036288476 chr7 159138663 16752708 0.10527113703349386 0.8030980444775785 chr8 146364022 15511080 0.10597604375752943 1.2816667153935248 chr9 141213431 12618124 0.08935498493765795 0.5682947276812845 chr10 135534747 13987229 0.10320031807046498 0.596416399675085 chr11 135006516 13552031 0.10038056977931346 0.5474273154742821 chr12 133851895 13926369 0.10404312169058197 0.49453412408572234 chr13 115169878 9600986 0.08336368993982958 0.448676817721088 chr14 107349540 9370090 0.08728579554230041 0.4912298295071431 chr15 102531392 8519009 0.08308683646858125 0.44787392212534016 chr16 90354753 8722234 0.0965332061723416 0.510779488434306 chr17 81195210 8052947 0.09918007478519977 0.4966037943180405 chr18 78077248 7963286 0.1019924011665985 0.8375799105776726 chr19 59128983 6121676 0.10353088602927603 0.7569749629396109 chr20 63025520 6162100 0.09777150589158169 0.4935009903898451 chr21 48129895 3840728 0.0797992183444406 0.5149611833120848 chr22 51304566 3408104 0.06642886327115602 0.6561709415969817 chrMT 16571 37127 2.2404803572506187 2.73929784561752 chrX 155270560 10270104 0.06614327918956434 0.4116398324937934 chrY 59373566 2690438 0.04531373439823372 0.4481791746483859