BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524972.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 = 971,774 number of mapped reads = 901,713 (92.79%) number of supplementary alignments = 2,010 (0.21%) number of secondary alignments = 0 number of mapped bases = 52,349,374 bp number of sequenced bases = 52,332,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,308 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6947 >>>>>>> ACTG content number of A's = 12,629,710 bp (24.13%) number of C's = 9,174,535 bp (17.53%) number of T's = 17,271,648 bp (33%) number of G's = 13,256,364 bp (25.33%) number of N's = 548 bp (0%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 250,529 number of insertions = 2,811 mapped reads with insertion percentage = 0.31% number of deletions = 9,493 mapped reads with deletion percentage = 1.05% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1719X There is a 1.56% of reference with a coverageData >= 1X There is a 0.09% 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 4181144 0.016774858907974397 0.26341786441219994 chr2 243199373 4434174 0.018232670361366433 0.19137581865200423 chr3 198022430 3480510 0.01757634223557402 0.14101780789759685 chr4 191154276 3429223 0.017939556842557894 0.15580024476079166 chr5 180915260 3159570 0.017464364255397803 0.14032091029753282 chr6 171115067 3034662 0.017734627658474986 0.15893095746011765 chr7 159138663 2864815 0.018002004955891833 0.20463169770003767 chr8 146364022 2686102 0.018352201335380083 0.18322683044852528 chr9 141213431 2167025 0.015345742856428438 0.15493945642875875 chr10 135534747 2510019 0.01851937643709919 0.18593617005658536 chr11 135006516 2401681 0.017789370995989557 0.16962807018834308 chr12 133851895 2371063 0.01771407868375715 0.1417854648500004 chr13 115169878 1675273 0.01454610379981474 0.12789942949487243 chr14 107349540 1591349 0.01482399458814635 0.1334369697122348 chr15 102531392 1506787 0.01469586017129271 0.1304227187805682 chr16 90354753 1538342 0.017025579163500122 0.1426666295845202 chr17 81195210 1407440 0.017334027462950093 0.14898874715627955 chr18 78077248 1403354 0.017973917318397287 0.22305889468651946 chr19 59128983 1011067 0.01709934703257115 0.2054605330979746 chr20 63025520 1115368 0.017697085244199492 0.14265297397283142 chr21 48129895 685522 0.014243164253734607 0.13445049419538205 chr22 51304566 602358 0.011740826342824926 0.11442405126994731 chrMT 16571 7607 0.45905497555971275 0.7310754084480785 chrX 155270560 2924017 0.01883175406851112 0.15482817629390266 chrY 59373566 160902 0.0027099938716835703 0.08476383046920023