BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525047.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 = 1,031,513 number of mapped reads = 882,013 (85.51%) number of supplementary alignments = 2,442 (0.24%) number of secondary alignments = 0 number of mapped bases = 50,852,873 bp number of sequenced bases = 50,836,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,733 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1062 >>>>>>> ACTG content number of A's = 12,614,465 bp (24.81%) number of C's = 10,052,123 bp (19.77%) number of T's = 16,707,877 bp (32.87%) number of G's = 11,456,604 bp (22.54%) number of N's = 4,981 bp (0.01%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 253,516 number of insertions = 3,491 mapped reads with insertion percentage = 0.39% number of deletions = 10,659 mapped reads with deletion percentage = 1.2% homopolymer indels = 43.62% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 0.1872X There is a 1.48% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% 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 4051689 0.0162554820675853 0.3305791431872604 chr2 243199373 4306998 0.01770974138161121 0.22948201195034493 chr3 198022430 3376528 0.017051240104466955 0.1412979986582678 chr4 191154276 3366098 0.017609326196814976 0.15586458312633508 chr5 180915260 3094054 0.017102227860712246 0.1425544140778443 chr6 171115067 2928514 0.017114296545259804 0.1508905791515355 chr7 159138663 2816930 0.017701103848032203 0.2051203250229539 chr8 146364022 2579201 0.017621823756660635 0.20197868039830588 chr9 141213431 2093512 0.014825162062665272 0.1512087392639423 chr10 135534747 2481908 0.01831196836926253 0.20141526550921207 chr11 135006516 2289640 0.0169594777188384 0.16071699555897806 chr12 133851895 2293335 0.017133377155400004 0.14523293932760734 chr13 115169878 1610704 0.013985462414052397 0.1285620297502731 chr14 107349540 1528707 0.01424046157999373 0.13039998664096425 chr15 102531392 1471906 0.014355661922545634 0.1301726629298517 chr16 90354753 1443809 0.015979336471651912 0.14397782520717173 chr17 81195210 1331739 0.016401694139346397 0.1434015010573656 chr18 78077248 1360067 0.017419504847301995 0.2461683191408532 chr19 59128983 991845 0.016774261109818174 0.23278077010938522 chr20 63025520 1107841 0.017577657431465856 0.14733959275393058 chr21 48129895 687221 0.014278464559293137 0.14374169964150418 chr22 51304566 593921 0.011576377042152544 0.11730178954705983 chrMT 16571 20949 1.2641964878402028 1.3504520454745448 chrX 155270560 2852719 0.018372568502361297 0.15804093560927704 chrY 59373566 173038 0.0029143945977575273 0.10359360124738273