BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525121.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 = 839,471 number of mapped reads = 735,273 (87.59%) number of supplementary alignments = 23,185 (2.76%) number of secondary alignments = 0 number of mapped bases = 56,138,916 bp number of sequenced bases = 56,116,282 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,505 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0784 >>>>>>> ACTG content number of A's = 14,724,882 bp (26.24%) number of C's = 10,871,564 bp (19.37%) number of T's = 16,755,303 bp (29.86%) number of G's = 13,762,409 bp (24.52%) number of N's = 2,124 bp (0%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 401,798 number of insertions = 4,951 mapped reads with insertion percentage = 0.66% number of deletions = 12,946 mapped reads with deletion percentage = 1.73% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 0.2135X There is a 1.68% of reference with a coverageData >= 1X There is a 0.09% 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 5409908 0.02170469216203076 0.3517839324277711 chr2 243199373 4532998 0.018639020093197362 0.2971229722792392 chr3 198022430 3557963 0.01796747469465959 0.1406437989619261 chr4 191154276 3395793 0.01776467192394901 0.14878379846446277 chr5 180915260 3311945 0.01830660940376174 0.1422335034749806 chr6 171115067 3060316 0.017884550166467807 0.15096589834703625 chr7 159138663 3176762 0.019962226275584583 0.28634719996433045 chr8 146364022 2687970 0.0183649640346724 0.2503705373037099 chr9 141213431 2274609 0.0161075967341945 0.1900496300440046 chr10 135534747 2574532 0.01899536507785712 0.21792834757909202 chr11 135006516 3044639 0.0225517929816069 0.2330597048000735 chr12 133851895 2567955 0.019185047772390523 0.14593956652451545 chr13 115169878 1881252 0.01633458359658938 0.13467080288273536 chr14 107349540 1560925 0.014540583965241025 0.13445824844164714 chr15 102531392 1552707 0.01514372300729127 0.12907385799851048 chr16 90354753 1299183 0.01437869018357009 0.1343212418683041 chr17 81195210 1836575 0.022619253032290943 0.18006454351776163 chr18 78077248 1515443 0.019409534004067357 0.3003620892084137 chr19 59128983 1196417 0.0202340195839323 0.26684175888578304 chr20 63025520 1139941 0.01808697492698196 0.14494866521469285 chr21 48129895 714298 0.014841046297732417 0.1364567083927372 chr22 51304566 681988 0.013292929911930255 0.12098832098899986 chrMT 16571 5462 0.3296119727234325 0.6432062533051949 chrX 155270560 3007881 0.01937186933569377 0.17108757579095513 chrY 59373566 151454 0.0025508658179635023 0.0765559314612818