BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525178.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 = 4,396,722 number of mapped reads = 4,064,878 (92.45%) number of supplementary alignments = 14,145 (0.32%) number of secondary alignments = 0 number of mapped bases = 235,585,028 bp number of sequenced bases = 235,510,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 285,224 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6663 >>>>>>> ACTG content number of A's = 59,705,708 bp (25.35%) number of C's = 47,101,404 bp (20%) number of T's = 72,673,453 bp (30.86%) number of G's = 56,024,097 bp (23.79%) number of N's = 5,477 bp (0%) GC percentage = 43.79% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,186,586 number of insertions = 13,887 mapped reads with insertion percentage = 0.34% number of deletions = 47,110 mapped reads with deletion percentage = 1.15% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0761X std coverageData = 0.661X There is a 6.14% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23470694 0.09416503720566458 1.2217427140757304 chr2 243199373 19575323 0.08049084485098569 0.983699585920386 chr3 198022430 18534477 0.09359786666591255 0.37847062110859636 chr4 191154276 12764182 0.06677424260182388 0.35578177698810237 chr5 180915260 10838078 0.05990693101289521 0.30060008917150555 chr6 171115067 14226735 0.0831413343630342 0.43781900839761484 chr7 159138663 16336770 0.10265745414739345 1.2383196111393284 chr8 146364022 13231843 0.09040365807930585 0.6127947014002821 chr9 141213431 8018856 0.056785363426231035 0.458003365644611 chr10 135534747 12816970 0.09456593444631582 0.6301279788319547 chr11 135006516 10812299 0.0800872381596752 0.5046325361683361 chr12 133851895 10688693 0.07985462589080267 0.3496680535437857 chr13 115169878 8271375 0.07181890910746645 0.32766629259431207 chr14 107349540 8875850 0.08268177022463254 0.3685748632083062 chr15 102531392 6594576 0.0643176286926837 0.3191114940000849 chr16 90354753 6442329 0.07130038859162174 0.38614014842428845 chr17 81195210 4501759 0.05544365240264789 0.30827880265241053 chr18 78077248 5145376 0.06590109323525338 0.8993509406282354 chr19 59128983 4365911 0.07383707242182738 0.8418544777248854 chr20 63025520 4579600 0.07266262936029723 0.3387754522515648 chr21 48129895 3042981 0.06322434320706496 0.3527615389393369 chr22 51304566 1972940 0.03845544663607524 0.2358484025969658 chrMT 16571 208582 12.587170357854083 7.159310966182083 chrX 155270560 9589681 0.061761102684243556 0.3637030008519945 chrY 59373566 679148 0.011438558364508543 0.30914030992494773