BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237806.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 = 4,443,421 number of mapped reads = 3,079,387 (69.3%) number of supplementary alignments = 18,954 (0.43%) number of secondary alignments = 0 number of mapped bases = 195,303,022 bp number of sequenced bases = 195,233,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,851 duplication rate = 5.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2477 >>>>>>> ACTG content number of A's = 52,690,997 bp (26.99%) number of C's = 38,584,919 bp (19.76%) number of T's = 58,659,579 bp (30.05%) number of G's = 45,128,507 bp (23.12%) number of N's = 169,436 bp (0.09%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,413,740 number of insertions = 12,752 mapped reads with insertion percentage = 0.41% number of deletions = 42,444 mapped reads with deletion percentage = 1.37% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0631X std coverageData = 0.409X There is a 4.3% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 20177940 0.08095442217574254 0.5432947127612651 chr2 243199373 19794490 0.08139202727303084 0.45780092263369254 chr3 198022430 13577898 0.06856747490675677 0.3613566010341146 chr4 191154276 5917726 0.030957853121737124 0.2596077052711066 chr5 180915260 21245692 0.11743449391720742 0.4753094904648334 chr6 171115067 6873280 0.040167590852768095 0.3161384236924091 chr7 159138663 6093776 0.03829224077369558 0.34370675260258443 chr8 146364022 13676510 0.0934417475901284 0.4599496505520787 chr9 141213431 5703363 0.04038824748900832 0.32884298161250464 chr10 135534747 7452290 0.05498435024931282 0.4411285868315876 chr11 135006516 7909280 0.05858443158402814 0.390277144923123 chr12 133851895 4378599 0.03271226754017939 0.25007244150349556 chr13 115169878 3684353 0.031990595665995235 0.2504165322112128 chr14 107349540 4962506 0.04622754787770865 0.30575339657446204 chr15 102531392 2496413 0.024347791942588667 0.21505652849026696 chr16 90354753 3557350 0.03937092274492743 0.295992445481712 chr17 81195210 9208315 0.11340958413679822 0.6089794655144458 chr18 78077248 3067329 0.039285823701163236 0.5066292526216749 chr19 59128983 2050952 0.03468606926657271 0.3737779919637872 chr20 63025520 3710589 0.05887438929500304 0.3725593289874713 chr21 48129895 1264944 0.02628187740696297 0.24067510210087334 chr22 51304566 4242506 0.08269256190569861 0.4136238609794354 chrMT 16571 361664 21.825116166797418 12.198240378138895 chrX 155270560 23356345 0.15042352523234281 0.5807674459723453 chrY 59373566 538912 0.009076631846569566 0.16058185917536272