BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716693.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 = 1,432,286 number of mapped reads = 1,281,643 (89.48%) number of supplementary alignments = 22,157 (1.55%) number of secondary alignments = 0 number of mapped bases = 99,601,853 bp number of sequenced bases = 99,559,249 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,947 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9456 >>>>>>> ACTG content number of A's = 24,873,180 bp (24.98%) number of C's = 19,451,581 bp (19.54%) number of T's = 30,901,618 bp (31.04%) number of G's = 24,327,608 bp (24.44%) number of N's = 5,262 bp (0.01%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 879,013 number of insertions = 9,111 mapped reads with insertion percentage = 0.7% number of deletions = 24,462 mapped reads with deletion percentage = 1.88% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.4209X There is a 2.84% of reference with a coverageData >= 1X There is a 0.24% 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 0.01% 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 9312554 0.03736220982173601 0.6762589348222525 chr2 243199373 8880631 0.036515846609522305 0.7512252079418715 chr3 198022430 7398952 0.03736421172086415 0.21611715265332557 chr4 191154276 4266155 0.02231786329488125 0.17721372913099134 chr5 180915260 5831123 0.03223123908950522 0.19987305918147263 chr6 171115067 7139123 0.04172118285761475 0.29062320580814643 chr7 159138663 5565664 0.034973675755966355 0.5976310176997365 chr8 146364022 7486569 0.05115033665855397 0.5658913967742977 chr9 141213431 4467703 0.03163794667661605 0.38755200689252617 chr10 135534747 4824679 0.0355973586610967 0.33360712617688365 chr11 135006516 4021170 0.02978500682144853 0.28978668631179316 chr12 133851895 3140667 0.023463747001863516 0.17493361211689537 chr13 115169878 3450925 0.029963780980995742 0.19033833638604103 chr14 107349540 2406307 0.02241562469666847 0.20787036151873106 chr15 102531392 1946074 0.018980274841094522 0.15901212589735317 chr16 90354753 2554063 0.028267057517162377 0.21403289763773858 chr17 81195210 3105566 0.03824814296311322 0.24914743233200476 chr18 78077248 3066294 0.039272567598694054 0.7934794373904043 chr19 59128983 1985903 0.03358594887383739 0.5709841722682284 chr20 63025520 1861423 0.029534433036014617 0.22094404516385413 chr21 48129895 2007572 0.04171153915877024 0.23156874785879436 chr22 51304566 1498347 0.02920494444880403 0.18889551957460216 chrMT 16571 3218 0.1941946774485547 0.5204804096760894 chrX 155270560 3157341 0.02033444717401676 0.21804409147856124 chrY 59373566 223830 0.0037698594691112203 0.10605931533496506