BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716373.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 = 462,382 number of mapped reads = 422,383 (91.35%) number of supplementary alignments = 9,178 (1.98%) number of secondary alignments = 0 number of mapped bases = 32,938,731 bp number of sequenced bases = 32,922,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,546 duplication rate = 1.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6265 >>>>>>> ACTG content number of A's = 8,415,290 bp (25.56%) number of C's = 6,549,395 bp (19.89%) number of T's = 10,033,004 bp (30.47%) number of G's = 7,922,557 bp (24.06%) number of N's = 2,433 bp (0.01%) GC percentage = 43.96% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 225,463 number of insertions = 2,788 mapped reads with insertion percentage = 0.65% number of deletions = 8,253 mapped reads with deletion percentage = 1.92% homopolymer indels = 42.39% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.1419X There is a 1.01% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 3386624 0.013587223921099078 0.27657002546988463 chr2 243199373 2785780 0.011454717031692348 0.14847235907902986 chr3 198022430 2180170 0.011009712384602088 0.10753380103327864 chr4 191154276 2156124 0.011279496567474116 0.11631277726028583 chr5 180915260 1995743 0.011031369050902616 0.1086644566528888 chr6 171115067 1854002 0.010834826134860467 0.11080635740059679 chr7 159138663 1834913 0.011530277843291923 0.15239456305785684 chr8 146364022 1723705 0.011776835430226153 0.15154592206991296 chr9 141213431 791270 0.005603362190102159 0.09606206135440981 chr10 135534747 1601393 0.01181536864491288 0.13870368444291967 chr11 135006516 1587982 0.011762261904455042 0.13359778677017453 chr12 133851895 1485866 0.011100821546082705 0.10839377239110044 chr13 115169878 1212883 0.010531251930300734 0.10565601823542924 chr14 107349540 548308 0.005107688398105851 0.07619824847500067 chr15 102531392 919719 0.008970121072773498 0.09784785903096464 chr16 90354753 785289 0.00869117532754475 0.09839697258589519 chr17 81195210 1007140 0.012403933680324246 0.12009503756598316 chr18 78077248 905228 0.011594004952633576 0.16498372006608844 chr19 59128983 694847 0.01175137749282784 0.21138155950286666 chr20 63025520 714522 0.011337026652060943 0.11131614521103164 chr21 48129895 451492 0.009380697797076017 0.1043441170244427 chr22 51304566 390632 0.007613981180544438 0.08979107256137764 chrMT 16571 5739 0.3463279222738519 0.6001788355127864 chrX 155270560 1818440 0.01171142810330561 0.11768822243714738 chrY 59373566 100920 0.001699746314715205 0.0626734338175615