BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,341,476 number of mapped reads = 1,031,201 (76.87%) number of supplementary alignments = 7,349 (0.55%) number of secondary alignments = 0 number of mapped bases = 66,847,890 bp number of sequenced bases = 66,815,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,518 duplication rate = 11.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4065 >>>>>>> ACTG content number of A's = 18,177,746 bp (27.21%) number of C's = 11,847,780 bp (17.73%) number of T's = 21,885,795 bp (32.76%) number of G's = 14,898,500 bp (22.3%) number of N's = 5,983 bp (0.01%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 562,104 number of insertions = 4,900 mapped reads with insertion percentage = 0.47% number of deletions = 18,354 mapped reads with deletion percentage = 1.76% homopolymer indels = 48.86% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2829X There is a 1.19% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 5372843 0.021555986414172265 0.38220374439854016 chr2 243199373 7079098 0.029108208268283652 0.33537776670682357 chr3 198022430 4316437 0.021797717561591382 0.2449813719802061 chr4 191154276 4382340 0.02292567078122804 0.25270268177203464 chr5 180915260 3614002 0.01997621427844174 0.23208468057280984 chr6 171115067 3498905 0.020447673377587492 0.25105443959976487 chr7 159138663 3952515 0.02483692476415992 0.3532803277725093 chr8 146364022 3713462 0.02537141265494877 0.3873118529068664 chr9 141213431 2458110 0.017407055282156553 0.24293257719431924 chr10 135534747 3195516 0.02357709790833195 0.2881558602126565 chr11 135006516 2833530 0.020988098085576848 0.2634015251900055 chr12 133851895 3230573 0.024135429685175545 0.2572567536505952 chr13 115169878 1725279 0.014980297191944582 0.20268946428501028 chr14 107349540 2149551 0.0200238491939509 0.23389647930980034 chr15 102531392 1924151 0.01876645739872526 0.22519062214161972 chr16 90354753 1986572 0.021986358592557938 0.24263119678310022 chr17 81195210 1630607 0.02008255166776464 0.2404974793223964 chr18 78077248 1640122 0.021006401250207998 0.3454266666975684 chr19 59128983 1220504 0.02064138326207978 0.29527827305432386 chr20 63025520 1313468 0.020840256454845593 0.23614421932982865 chr21 48129895 1067804 0.022185878444156173 0.2459479026885221 chr22 51304566 658052 0.012826382743399487 0.1832277414076185 chrMT 16571 17042 1.02842314887454 1.945095594213322 chrX 155270560 3674963 0.023668124852515505 0.26193058692256765 chrY 59373566 192444 0.003241240386336236 0.08571252948301213