BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524773.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 = 1,254,612 number of mapped reads = 1,125,968 (89.75%) number of supplementary alignments = 3,859 (0.31%) number of secondary alignments = 0 number of mapped bases = 63,950,392 bp number of sequenced bases = 63,929,676 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,709 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2929 >>>>>>> ACTG content number of A's = 16,321,099 bp (25.53%) number of C's = 11,685,002 bp (18.28%) number of T's = 19,845,254 bp (31.04%) number of G's = 16,070,600 bp (25.14%) number of N's = 7,721 bp (0.01%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 328,312 number of insertions = 5,341 mapped reads with insertion percentage = 0.47% number of deletions = 12,809 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2021X There is a 1.87% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 5082446 0.020390906067190902 0.2632394136904558 chr2 243199373 5356008 0.022023115988872223 0.320821925895514 chr3 198022430 4217751 0.02129935987554541 0.16079120063001678 chr4 191154276 4089700 0.021394760742888118 0.17674399213590378 chr5 180915260 3799111 0.020999394965355602 0.1573948684017749 chr6 171115067 3632704 0.021229597508207736 0.17251263941471504 chr7 159138663 3510000 0.02205623657903925 0.23177777303721736 chr8 146364022 3156509 0.02156615373687941 0.1906517155342939 chr9 141213431 2755309 0.01951166387282241 0.17749269286028177 chr10 135534747 3111742 0.022958998108433402 0.23688071074153147 chr11 135006516 2881154 0.02134085142971914 0.17854001724438087 chr12 133851895 2884376 0.02154901131582784 0.16152173379624302 chr13 115169878 1987926 0.017260815367018102 0.14343062766047018 chr14 107349540 1933387 0.01801020293147041 0.1506241397216828 chr15 102531392 1841466 0.01796002145372219 0.14596680446467378 chr16 90354753 1910435 0.021143713380523545 0.17186090719383174 chr17 81195210 1833999 0.022587527022837922 0.16768571108705144 chr18 78077248 1650213 0.02113564504732544 0.2550660058847511 chr19 59128983 1421868 0.02404688746295535 0.23067073282461995 chr20 63025520 1389424 0.022045419061992665 0.1662294543801114 chr21 48129895 866687 0.018007248925018433 0.15852880256646865 chr22 51304566 809404 0.01577645155403907 0.1379912500071475 chrMT 16571 20266 1.2229799046527066 1.3800790325212675 chrX 155270560 3588191 0.023109280986685434 0.1757240612593303 chrY 59373566 220316 0.0037106748818152508 0.11020853203530853