BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524742.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 = 936,386 number of mapped reads = 846,992 (90.45%) number of supplementary alignments = 3,310 (0.35%) number of secondary alignments = 0 number of mapped bases = 48,310,486 bp number of sequenced bases = 48,294,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,835 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.525 >>>>>>> ACTG content number of A's = 12,100,491 bp (25.06%) number of C's = 8,823,122 bp (18.27%) number of T's = 15,763,344 bp (32.64%) number of G's = 11,601,598 bp (24.02%) number of N's = 6,130 bp (0.01%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 249,309 number of insertions = 3,866 mapped reads with insertion percentage = 0.45% number of deletions = 9,826 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 0.1633X There is a 1.45% 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 3831809 0.015373317765976599 0.21486288506919365 chr2 243199373 4049704 0.01665178635143932 0.2394713685712039 chr3 198022430 3169700 0.016006772566117888 0.13600294602702456 chr4 191154276 3132821 0.016388966365575835 0.14737574805655548 chr5 180915260 2886858 0.01595696239222717 0.13350747346991904 chr6 171115067 2748585 0.016062787738031273 0.1412158131639685 chr7 159138663 2628987 0.01652010234621614 0.18459236395428158 chr8 146364022 2439792 0.01666934241531023 0.15687895157673432 chr9 141213431 2035386 0.014413543992143353 0.145044518314158 chr10 135534747 2389135 0.017627472311583684 0.19456248694657305 chr11 135006516 2190151 0.01622255773195421 0.14956545012880082 chr12 133851895 2178038 0.016271999735229747 0.13585064447483294 chr13 115169878 1521759 0.01321316846406662 0.12179520189033448 chr14 107349540 1440506 0.013418837192967943 0.12461934863921763 chr15 102531392 1398374 0.013638496198315536 0.12516163228321697 chr16 90354753 1440501 0.015942725226640815 0.14257535893323334 chr17 81195210 1335714 0.01645065022924382 0.13920018141450172 chr18 78077248 1276295 0.016346567440491754 0.20255822952706465 chr19 59128983 1045378 0.01767962083839663 0.17857745801057937 chr20 63025520 1050972 0.016675340401792797 0.1402204870755688 chr21 48129895 646708 0.013436721605147903 0.13121653429079475 chr22 51304566 591545 0.011530065374688094 0.11413716742953985 chrMT 16571 16982 1.0248023655784202 1.137435937347234 chrX 155270560 2701081 0.017395963536165515 0.1459841005480775 chrY 59373566 163705 0.0027572034329216475 0.08846826096926519