BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174025.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,581,030 number of mapped reads = 5,452,178 (97.69%) number of supplementary alignments = 558,540 (10.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,728,517 number of mapped paired reads (second in pair) = 2,723,661 number of mapped paired reads (both in pair) = 5,363,386 number of mapped paired reads (singletons) = 88,792 number of mapped bases = 645,688,782 bp number of sequenced bases = 645,291,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,256,501 duplication rate = 65.33% >>>>>>> Insert size mean insert size = 1,097,333.5033 std insert size = 9,341,335.2202 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.7731 >>>>>>> ACTG content number of A's = 194,701,568 bp (30.17%) number of C's = 125,906,648 bp (19.51%) number of T's = 194,331,085 bp (30.12%) number of G's = 130,344,503 bp (20.2%) number of N's = 7,561 bp (0%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 6,450,044 number of insertions = 68,341 mapped reads with insertion percentage = 1.21% number of deletions = 160,143 mapped reads with deletion percentage = 2.87% homopolymer indels = 42.39% >>>>>>> Coverage mean coverageData = 0.2086X std coverageData = 2.9685X There is a 4.32% of reference with a coverageData >= 1X There is a 3.41% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 2.17% of reference with a coverageData >= 4X There is a 1.66% of reference with a coverageData >= 5X There is a 1.35% of reference with a coverageData >= 6X There is a 1% of reference with a coverageData >= 7X There is a 0.82% of reference with a coverageData >= 8X There is a 0.6% of reference with a coverageData >= 9X There is a 0.5% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 58563880 0.23495981580723926 1.6970091423979796 chr2 243199373 48597763 0.1998268433035804 8.693275224635668 chr3 198022430 39159672 0.19775371911151682 1.28860798361108 chr4 191154276 41315109 0.2161348930536087 1.7601495312590851 chr5 180915260 32422280 0.17921252192877482 1.2133294597481425 chr6 171115067 32752604 0.1914068969741864 1.3199235318197093 chr7 159138663 57132178 0.35900878468483804 3.211362922101772 chr8 146364022 63655355 0.4349112174575252 2.2550131691588327 chr9 141213431 22527635 0.15952898276368627 1.4185498491238935 chr10 135534747 29742768 0.2194475487529408 3.530300015094768 chr11 135006516 26477497 0.19612014134191863 1.2975664111575331 chr12 133851895 24846345 0.18562564990208022 1.2419715726147182 chr13 115169878 16519345 0.14343459667466177 1.0955456023667534 chr14 107349540 21995711 0.20489804613974125 1.3079260764908593 chr15 102531392 14549465 0.14190254044341855 1.0680887421429963 chr16 90354753 14684392 0.16251930875180412 1.5416739524607674 chr17 81195210 16097766 0.1982600451430571 1.3645601984776603 chr18 78077248 11601187 0.14858601317505454 1.7930408037615941 chr19 59128983 8615377 0.1457048060508668 1.3746612894266625 chr20 63025520 24066134 0.38184744846214674 1.7966272020594345 chr21 48129895 7701431 0.16001345941020648 1.2520287339733385 chr22 51304566 6342800 0.12363032171444545 0.9623475999377682 chrMT 16571 1219993 73.6221712630499 54.420930937376326 chrX 155270560 23862939 0.15368617850029007 1.133907303342508 chrY 59373566 1239156 0.02087049984499836 0.9539027774421529