BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524478.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 = 1,567,376 number of mapped reads = 1,438,447 (91.77%) number of supplementary alignments = 5,055 (0.32%) number of secondary alignments = 0 number of mapped bases = 83,224,832 bp number of sequenced bases = 83,198,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,117 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3825 >>>>>>> ACTG content number of A's = 20,163,976 bp (24.24%) number of C's = 15,371,416 bp (18.48%) number of T's = 26,966,889 bp (32.41%) number of G's = 20,694,526 bp (24.87%) number of N's = 1,562 bp (0%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 417,462 number of insertions = 6,035 mapped reads with insertion percentage = 0.42% number of deletions = 16,528 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.58% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.2476X There is a 2.45% of reference with a coverageData >= 1X There is a 0.17% 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 6968908 0.027959440871362963 0.37128054874211824 chr2 243199373 6533902 0.02686644262031054 0.35343910484274105 chr3 198022430 4757547 0.02402529349831734 0.16911112088333435 chr4 191154276 5045155 0.026393105639970094 0.20117946408830964 chr5 180915260 4717259 0.026074411854478168 0.17327734546188878 chr6 171115067 4422753 0.025846660247633248 0.20435634352981827 chr7 159138663 4683010 0.02942722976125544 0.32467660175996965 chr8 146364022 4374063 0.029884823744458184 0.29399556881518585 chr9 141213431 2688051 0.019035377732589755 0.18187416566236916 chr10 135534747 3635273 0.02682170499052911 0.2612814622287688 chr11 135006516 2928126 0.021688775377330678 0.1995419511594152 chr12 133851895 4093287 0.030580717590886555 0.18957366634027784 chr13 115169878 2525656 0.021929831340100923 0.16012778266214703 chr14 107349540 2746161 0.02558148828583709 0.17496189622779929 chr15 102531392 3017823 0.029433161309270043 0.18839202374924208 chr16 90354753 2801754 0.03100837429105694 0.19776115996406113 chr17 81195210 3569699 0.04396440381150563 0.23540140381244462 chr18 78077248 1564985 0.02004405944225903 0.30002370353994656 chr19 59128983 2302805 0.03894545252029787 0.31320099960368475 chr20 63025520 3324136 0.05274269851323718 0.26045580249154876 chr21 48129895 1048587 0.021786604770278432 0.18330343850709674 chr22 51304566 748069 0.014580943926121507 0.12876158124851167 chrMT 16571 10596 0.6394303300947438 0.9241617254978484 chrX 155270560 4439365 0.02859115726767521 0.19433484385719813 chrY 59373566 277862 0.0046798940794629046 0.18698464113927477