BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716429.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 = 1,747,534 number of mapped reads = 1,607,624 (91.99%) number of supplementary alignments = 5,682 (0.33%) number of secondary alignments = 0 number of mapped bases = 93,544,490 bp number of sequenced bases = 93,513,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,786 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4017 >>>>>>> ACTG content number of A's = 21,959,071 bp (23.48%) number of C's = 17,508,657 bp (18.72%) number of T's = 30,137,795 bp (32.23%) number of G's = 23,906,354 bp (25.56%) number of N's = 1,945 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 469,657 number of insertions = 6,307 mapped reads with insertion percentage = 0.39% number of deletions = 19,016 mapped reads with deletion percentage = 1.17% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.2805X There is a 2.72% 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 7878157 0.03160737160209522 0.4435443217913881 chr2 243199373 7375276 0.030326048579080837 0.4178138467568772 chr3 198022430 5332527 0.026928903963051053 0.17985329601428734 chr4 191154276 5705857 0.029849486600027716 0.22231042356566405 chr5 180915260 5283068 0.02920189264299761 0.1851458802392237 chr6 171115067 4957517 0.028971832153155748 0.2204773891889404 chr7 159138663 5280116 0.0331793412138947 0.36179917457491817 chr8 146364022 4973506 0.0339803862454668 0.3465286163124054 chr9 141213431 3107020 0.022002298067525884 0.2041569884106928 chr10 135534747 4177131 0.030819631809988916 0.29621815636922694 chr11 135006516 3349536 0.024810180273076597 0.21926054861884425 chr12 133851895 4640778 0.03467099214396629 0.20401176051993525 chr13 115169878 2792905 0.024250307879982298 0.17106500724060944 chr14 107349540 3156160 0.029400778056431355 0.1913559779827127 chr15 102531392 3438960 0.03354055702277016 0.2015657770036303 chr16 90354753 3239792 0.03585635389872628 0.21546880822077397 chr17 81195210 4134157 0.05091626710491912 0.25630728823342636 chr18 78077248 1724393 0.022085729763426088 0.31208446995412137 chr19 59128983 2464890 0.04168666320541992 0.36043005750192797 chr20 63025520 3125804 0.049595846254025355 0.2541478557410864 chr21 48129895 1176968 0.024453990601890987 0.19548657536223854 chr22 51304566 874994 0.01705489526994537 0.1410357029235427 chrMT 16571 21827 1.3171806167400881 1.4959376222479062 chrX 155270560 4997685 0.032186945162044886 0.21431007720992204 chrY 59373566 335466 0.00565009014280867 0.22290141288856258