BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524925.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 = 1,608,119 number of mapped reads = 1,496,895 (93.08%) number of supplementary alignments = 6,841 (0.43%) number of secondary alignments = 0 number of mapped bases = 87,617,438 bp number of sequenced bases = 87,588,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,989 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9531 >>>>>>> ACTG content number of A's = 21,449,430 bp (24.49%) number of C's = 15,894,648 bp (18.15%) number of T's = 28,619,833 bp (32.68%) number of G's = 21,624,270 bp (24.69%) number of N's = 779 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 428,336 number of insertions = 6,631 mapped reads with insertion percentage = 0.44% number of deletions = 16,832 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.2477X There is a 2.48% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 9050776 0.036311949650067274 0.4182312879939237 chr2 243199373 7586742 0.031195565623436044 0.3119231556125401 chr3 198022430 5397440 0.02725671026256975 0.18386105481613593 chr4 191154276 3730490 0.019515597966534633 0.18468406324020128 chr5 180915260 5161216 0.028528361841892166 0.1881336688448399 chr6 171115067 5504988 0.03217126403018619 0.20837534404863173 chr7 159138663 5083429 0.031943393919301684 0.2863445691761274 chr8 146364022 7429527 0.050760609735089134 0.32899434228201 chr9 141213431 3351830 0.023735915034880782 0.20708837703106178 chr10 135534747 3795551 0.02800426520883239 0.25973946644595153 chr11 135006516 4594053 0.034028379785757894 0.23001179448628964 chr12 133851895 2976218 0.022235157746552634 0.16990838072404496 chr13 115169878 1924783 0.016712555690994134 0.1443304141873026 chr14 107349540 1677103 0.015622824280383502 0.14318128774869235 chr15 102531392 2432785 0.02372722102514711 0.17217098007404932 chr16 90354753 2697208 0.02985131285788585 0.19806029149071874 chr17 81195210 2440599 0.030058411081146288 0.19878325051441262 chr18 78077248 2190472 0.028055189650127012 0.31103895511648877 chr19 59128983 2032189 0.03436874603441091 0.3043100155373742 chr20 63025520 1785300 0.02832662070856377 0.1928274275983802 chr21 48129895 746043 0.015500615573750992 0.16064456135748983 chr22 51304566 2202002 0.04292019544615191 0.23532786710621692 chrMT 16571 7365 0.4444511495986965 0.7986897310220766 chrX 155270560 3597066 0.02316643927863724 0.18345830647708997 chrY 59373566 222263 0.003743467252750155 0.1409800934635089