BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716656.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,652,067 number of mapped reads = 1,535,150 (92.92%) number of supplementary alignments = 10,078 (0.61%) number of secondary alignments = 0 number of mapped bases = 90,605,090 bp number of sequenced bases = 90,577,894 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,513 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8284 >>>>>>> ACTG content number of A's = 22,811,392 bp (25.18%) number of C's = 17,721,366 bp (19.56%) number of T's = 28,381,368 bp (31.33%) number of G's = 21,662,683 bp (23.92%) number of N's = 1,085 bp (0%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 452,325 number of insertions = 6,072 mapped reads with insertion percentage = 0.39% number of deletions = 17,111 mapped reads with deletion percentage = 1.11% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.292X There is a 2.63% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7010623 0.02812680254064442 0.38515265016353945 chr2 243199373 8651874 0.03557523152002534 0.31498358744216765 chr3 198022430 6476014 0.03270343667634015 0.20184889836848507 chr4 191154276 4886216 0.025561635879910945 0.1931244021901185 chr5 180915260 4735989 0.026177940987399295 0.17510321792636657 chr6 171115067 4837932 0.028272974933294448 0.19550474816630548 chr7 159138663 5939334 0.037321753796561684 0.7265270011221788 chr8 146364022 7246376 0.04950927079607036 0.33153716457434007 chr9 141213431 3637442 0.02575847052395462 0.19833604573314131 chr10 135534747 4206281 0.031034705808688307 0.3471726971459486 chr11 135006516 2940633 0.021781415350352423 0.20216172416671846 chr12 133851895 4716342 0.03523552654969883 0.2149125628906034 chr13 115169878 2948836 0.02560422960593915 0.1735897957108962 chr14 107349540 2812202 0.02619668421494866 0.17848020599988362 chr15 102531392 2086120 0.020346158959784727 0.15599222080381916 chr16 90354753 2669249 0.029541877005629134 0.19477318491289045 chr17 81195210 3673266 0.04523993472028707 0.24186295061356278 chr18 78077248 2074414 0.026568738693249026 0.30573709585760545 chr19 59128983 1777189 0.030056140150423356 0.3375780031691944 chr20 63025520 1967214 0.03121297531539605 0.19904787740479865 chr21 48129895 687222 0.014278485336400588 0.14415469433636513 chr22 51304566 1336565 0.026051579892518727 0.17479588931246776 chrMT 16571 10445 0.6303180254661759 0.9005053885144897 chrX 155270560 3078347 0.019825696513234705 0.169676193085517 chrY 59373566 198965 0.003351070407325711 0.10095649793643571