BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082949.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,954,094 number of mapped reads = 1,790,943 (91.65%) number of supplementary alignments = 17,001 (0.87%) number of secondary alignments = 0 number of mapped bases = 120,243,100 bp number of sequenced bases = 120,197,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,364 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.008 >>>>>>> ACTG content number of A's = 33,414,050 bp (27.8%) number of C's = 21,808,687 bp (18.14%) number of T's = 38,700,969 bp (32.2%) number of G's = 26,267,691 bp (21.85%) number of N's = 5,666 bp (0%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 873,099 number of insertions = 10,130 mapped reads with insertion percentage = 0.56% number of deletions = 28,011 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3317X There is a 3.16% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 11735255 0.04708214949642994 0.4877162258465043 chr2 243199373 12699438 0.05221821850667353 0.45398986486932447 chr3 198022430 7996152 0.040380031696409344 0.23688372185916579 chr4 191154276 7937715 0.04152517624036828 0.250296506990443 chr5 180915260 6211172 0.034331940821354705 0.2205851264749176 chr6 171115067 6701661 0.03916464585786592 0.27924429627281966 chr7 159138663 7627758 0.04793151994748127 0.4170628899431375 chr8 146364022 9366165 0.06399226307131681 0.46141845936615655 chr9 141213431 3613447 0.02558855042619848 0.31434087269721694 chr10 135534747 4556611 0.03361950422942096 0.24930997898761495 chr11 135006516 5324017 0.03943525955443514 0.3102862819176546 chr12 133851895 2866107 0.02141252464150769 0.1773578459623097 chr13 115169878 4109154 0.03567906879262302 0.2260624586096822 chr14 107349540 2459230 0.022908621685756643 0.20277610353836206 chr15 102531392 2414536 0.02354923651090195 0.19190120502962177 chr16 90354753 4263257 0.04718353886706989 0.2700547990321897 chr17 81195210 3167193 0.039007140938486395 0.27203339600591353 chr18 78077248 3394422 0.04347517473976542 0.6556099141948072 chr19 59128983 1836083 0.03105216607564517 0.3630749897862006 chr20 63025520 2319546 0.036803282225993536 0.2393886101071056 chr21 48129895 2970508 0.06171856389879928 0.30369484725215723 chr22 51304566 1497135 0.02918132082045095 0.1995995059107941 chrMT 16571 14027 0.8464787882445236 1.1139368661272773 chrX 155270560 4952132 0.03189356694533722 0.23372991347149255 chrY 59373566 210379 0.003543310839709375 0.08301625958495389