BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174028.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,457,510 number of mapped reads = 3,369,044 (97.44%) number of supplementary alignments = 334,910 (9.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,688,166 number of mapped paired reads (second in pair) = 1,680,878 number of mapped paired reads (both in pair) = 3,306,262 number of mapped paired reads (singletons) = 62,782 number of mapped bases = 398,073,428 bp number of sequenced bases = 397,853,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,622,230 duplication rate = 65.08% >>>>>>> Insert size mean insert size = 911,806.7031 std insert size = 8,971,376.5082 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.6948 >>>>>>> ACTG content number of A's = 119,695,309 bp (30.09%) number of C's = 77,906,546 bp (19.58%) number of T's = 119,533,058 bp (30.04%) number of G's = 80,713,522 bp (20.29%) number of N's = 4,569 bp (0%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,930,005 number of insertions = 41,603 mapped reads with insertion percentage = 1.2% number of deletions = 89,211 mapped reads with deletion percentage = 2.59% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 0.1286X std coverageData = 2.0152X There is a 2.7% of reference with a coverageData >= 1X There is a 2.13% of reference with a coverageData >= 2X There is a 1.64% of reference with a coverageData >= 3X There is a 1.35% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% 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 0.01% 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% 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 34024096 0.13650556160499996 1.5119094031018265 chr2 243199373 41928694 0.17240461388853992 5.780121439831785 chr3 198022430 30834506 0.1557121887656868 1.1490461068715991 chr4 191154276 22751910 0.11902380881084763 1.1714951470846802 chr5 180915260 24039889 0.1328792772925844 1.0512438733691638 chr6 171115067 22902515 0.1338427725946541 1.0865000538349994 chr7 159138663 28939162 0.18184871893764748 1.8296272876568607 chr8 146364022 15968178 0.10909906534271106 1.0489321752167466 chr9 141213431 15229247 0.10784559862439713 1.0599589324000738 chr10 135534747 19540413 0.14417271904451187 1.8179860635522453 chr11 135006516 18586256 0.13766932553092476 1.0822887391116647 chr12 133851895 13876051 0.10366719873484047 0.933231727737824 chr13 115169878 12491083 0.10845789903502373 0.9527761262104495 chr14 107349540 10465817 0.09749289098025013 0.9035355224859482 chr15 102531392 13171941 0.1284673965998628 1.020264715717792 chr16 90354753 15551561 0.17211668986577827 1.5845180150392832 chr17 81195210 9446977 0.11634894472223177 1.07375141797213 chr18 78077248 6694886 0.08574695153189825 1.436303186015463 chr19 59128983 6949546 0.11753197243389084 1.554556468744378 chr20 63025520 9700557 0.15391474754988138 1.1328807909554666 chr21 48129895 6314057 0.13118784073806936 1.0776202700506348 chr22 51304566 3441022 0.06707048257654104 0.713546313010326 chrMT 16571 1250644 75.47184840987266 62.63187144548817 chrX 155270560 13468044 0.08673919898273053 0.8489047682423113 chrY 59373566 506376 0.008528643874952701 0.5071838993793876