BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038486.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 10,921,602 number of mapped reads = 10,198,942 (93.38%) number of supplementary alignments = 164,910 (1.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,179,998 number of mapped paired reads (second in pair) = 5,018,944 number of mapped paired reads (both in pair) = 10,020,652 number of mapped paired reads (singletons) = 178,290 number of mapped bases = 1,460,147,858 bp number of sequenced bases = 1,459,160,585 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,190,450 duplication rate = 7.39% >>>>>>> Insert size mean insert size = 98,439.024 std insert size = 2,999,074.6491 median insert size = 271 >>>>>>> Mapping quality mean mapping quality = 53.8403 >>>>>>> ACTG content number of A's = 419,073,606 bp (28.72%) number of C's = 305,021,133 bp (20.9%) number of T's = 419,144,520 bp (28.73%) number of G's = 315,889,499 bp (21.65%) number of N's = 31,827 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 20,558,068 number of insertions = 242,133 mapped reads with insertion percentage = 2.23% number of deletions = 489,866 mapped reads with deletion percentage = 4.62% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.4717X std coverageData = 5.6773X There is a 21.49% of reference with a coverageData >= 1X There is a 10.54% of reference with a coverageData >= 2X There is a 5.24% of reference with a coverageData >= 3X There is a 2.91% of reference with a coverageData >= 4X There is a 1.63% of reference with a coverageData >= 5X There is a 0.96% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 94073294 0.3774245120135528 3.3858928486602875 chr2 243199373 153940586 0.6329810151278639 7.024020141834445 chr3 198022430 99747983 0.5037206290216719 1.236733629690955 chr4 191154276 83512023 0.43688284012019696 4.69205978624052 chr5 180915260 63751947 0.3523856804561428 1.0398923487825917 chr6 171115067 105839368 0.6185274614070075 7.3055848520398206 chr7 159138663 83049972 0.5218717465283719 4.991386717459269 chr8 146364022 67072510 0.45825817768249083 1.6253273873568423 chr9 141213431 61430189 0.43501661679759057 7.704765917363816 chr10 135534747 65378760 0.4823763754102112 15.686816550960012 chr11 135006516 66757587 0.49447677769864085 2.751783502306645 chr12 133851895 60738323 0.4537726044147526 1.1602713034125152 chr13 115169878 75333209 0.6541051384981063 1.4972325281160626 chr14 107349540 28672091 0.2670909535336621 0.9064977064021619 chr15 102531392 27979067 0.27288293325813817 0.8449694816446559 chr16 90354753 64007004 0.7083966462727201 12.248418971408885 chr17 81195210 35002210 0.43108712940085997 3.1490005934864103 chr18 78077248 23435280 0.30015504644835844 6.122356742558258 chr19 59128983 19012130 0.321536563549554 2.1234632932539435 chr20 63025520 60973075 0.9674346994677712 2.4022928079590096 chr21 48129895 12836698 0.26670945365660986 2.451019629707814 chr22 51304566 10190224 0.19862216552031645 0.7974758769716022 chrMT 16571 1037556 62.61275722647999 28.744049242705433 chrX 155270560 76799976 0.49462033240557646 1.406550140667477 chrY 59373566 19576796 0.32972242226448045 8.890920800351665