BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525013.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 = 1,047,145 number of mapped reads = 976,199 (93.22%) number of supplementary alignments = 2,916 (0.28%) number of secondary alignments = 0 number of mapped bases = 57,004,002 bp number of sequenced bases = 56,985,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,216 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6945 >>>>>>> ACTG content number of A's = 13,393,649 bp (23.5%) number of C's = 10,721,904 bp (18.82%) number of T's = 18,184,260 bp (31.91%) number of G's = 14,685,083 bp (25.77%) number of N's = 566 bp (0%) GC percentage = 44.59% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 273,642 number of insertions = 3,062 mapped reads with insertion percentage = 0.31% number of deletions = 11,005 mapped reads with deletion percentage = 1.12% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.1949X There is a 1.72% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5991573 0.024038347330737442 0.3534335708790665 chr2 243199373 5296540 0.02177859233214388 0.22632578690408156 chr3 198022430 3082620 0.015567024402235646 0.13295118484162508 chr4 191154276 3587824 0.018769258397337656 0.15216185065635077 chr5 180915260 2420908 0.013381447203513955 0.12458454987354826 chr6 171115067 4569561 0.026704609244024083 0.22120151623724 chr7 159138663 3520640 0.022123096509865738 0.2543088216221147 chr8 146364022 4008877 0.027389770691051384 0.20215895641014667 chr9 141213431 1567961 0.011103483492303222 0.14655672902022013 chr10 135534747 2888385 0.021311029562035483 0.19242985456944592 chr11 135006516 2367757 0.017538094235392314 0.17773752924923972 chr12 133851895 2392492 0.017874173540837805 0.14213342381641317 chr13 115169878 1081536 0.009390788796355241 0.10168022630122209 chr14 107349540 1264009 0.011774703459372066 0.11506403468684324 chr15 102531392 1566933 0.015282470757833854 0.13591510635322254 chr16 90354753 1823047 0.020176547879003113 0.1556568177194618 chr17 81195210 1499031 0.018462061986168888 0.18073738251190274 chr18 78077248 1114791 0.014278051910846037 0.21920061514725075 chr19 59128983 1428772 0.02416364915324182 0.23694380649432537 chr20 63025520 1386353 0.02199669276826276 0.15662911211587427 chr21 48129895 805753 0.01674121665962496 0.1400564715845278 chr22 51304566 784324 0.015287606175247638 0.12928899326048282 chrMT 16571 6443 0.38881177961499 0.6867754169693948 chrX 155270560 2384171 0.015354945586594136 0.14704614328785023 chrY 59373566 163701 0.002757136062873502 0.08022529818963439