BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716618.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 = 972,395 number of mapped reads = 868,030 (89.27%) number of supplementary alignments = 3,428 (0.35%) number of secondary alignments = 0 number of mapped bases = 49,937,551 bp number of sequenced bases = 49,922,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,649 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0199 >>>>>>> ACTG content number of A's = 12,352,514 bp (24.74%) number of C's = 10,057,560 bp (20.15%) number of T's = 16,151,316 bp (32.35%) number of G's = 11,359,445 bp (22.75%) number of N's = 1,386 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 257,939 number of insertions = 3,417 mapped reads with insertion percentage = 0.39% number of deletions = 9,687 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.1766X There is a 1.49% 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 4000031 0.01604822882266761 0.30262905605358753 chr2 243199373 4208983 0.01730671813861954 0.2230709031778881 chr3 198022430 3334433 0.016838663175681664 0.1379420713509336 chr4 191154276 3222544 0.016858341165227192 0.1443562174387702 chr5 180915260 3011230 0.01664442236658201 0.1372866687983534 chr6 171115067 2913646 0.01702740764493871 0.15670551645465353 chr7 159138663 2743990 0.01724276142749798 0.19525724111017562 chr8 146364022 2515823 0.017188807506259975 0.17207894845985114 chr9 141213431 2061536 0.014598724677966362 0.15097914651901828 chr10 135534747 2417551 0.01783713072486128 0.17382558802951503 chr11 135006516 2236361 0.016564837507546674 0.1552415965602743 chr12 133851895 2239504 0.01673120877369723 0.1395323027380825 chr13 115169878 1570459 0.013636022085566505 0.12405405269249152 chr14 107349540 1512705 0.01409139713127788 0.12885917870123367 chr15 102531392 1447735 0.014119919487682368 0.1261793245729001 chr16 90354753 1444902 0.01599143323428708 0.13998505348075738 chr17 81195210 1360910 0.01676096410120745 0.14316207805999723 chr18 78077248 1333170 0.01707501268487332 0.23767756515136576 chr19 59128983 1044343 0.01766211673216162 0.21819671354259496 chr20 63025520 1044973 0.016580156736509276 0.1382281273616102 chr21 48129895 667546 0.013869674970203031 0.13151274055255 chr22 51304566 582618 0.011356065267173296 0.11310402635866115 chrMT 16571 24880 1.5014181401243136 1.4353219524488998 chrX 155270560 2836874 0.01827052082506819 0.1544200976481183 chrY 59373566 160804 0.0027083433055040016 0.07951264107145055