BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524663.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 = 1,406,660 number of mapped reads = 1,295,676 (92.11%) number of supplementary alignments = 5,086 (0.36%) number of secondary alignments = 0 number of mapped bases = 76,268,815 bp number of sequenced bases = 76,245,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,869 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7405 >>>>>>> ACTG content number of A's = 19,689,751 bp (25.82%) number of C's = 14,870,240 bp (19.5%) number of T's = 23,862,112 bp (31.3%) number of G's = 17,813,005 bp (23.36%) number of N's = 10,391 bp (0.01%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 383,331 number of insertions = 5,640 mapped reads with insertion percentage = 0.43% number of deletions = 14,608 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2484X There is a 2.25% of reference with a coverageData >= 1X There is a 0.15% 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 6101031 0.024477495684955584 0.44090489202492317 chr2 243199373 6457735 0.026553255135242475 0.3414573429527008 chr3 198022430 5059838 0.02555184278871843 0.17214077982148202 chr4 191154276 4975567 0.02602906460747967 0.1944095851903697 chr5 180915260 4588342 0.025361829621227086 0.17137963226401567 chr6 171115067 4294860 0.025099250903487066 0.18882292102564094 chr7 159138663 4211673 0.02646542908306324 0.27733905600630276 chr8 146364022 3866245 0.02641526891082564 0.2537262579262021 chr9 141213431 3143234 0.02225874676184307 0.20680477892830887 chr10 135534747 3659334 0.02699923142218283 0.24867435000105412 chr11 135006516 3504248 0.02595613977624606 0.21746411339153057 chr12 133851895 3436924 0.025677066432268292 0.17469916199454597 chr13 115169878 2386135 0.020718394787220318 0.15671075683127988 chr14 107349540 2293692 0.02136657502211933 0.1602730449555036 chr15 102531392 2218001 0.02163240893091552 0.16086449868587177 chr16 90354753 2230014 0.024680649616739034 0.18205525432201397 chr17 81195210 2108503 0.025968317589177982 0.18116563785041903 chr18 78077248 2047104 0.02621895689766115 0.37446033730849837 chr19 59128983 1596461 0.026999635694731974 0.3329513884161889 chr20 63025520 1637682 0.025984426625912806 0.1750796597895208 chr21 48129895 1005095 0.020882966813037925 0.17601435768823542 chr22 51304566 936324 0.018250305440650254 0.1442815178520178 chrMT 16571 14695 0.8867901756079899 1.0918914320526591 chrX 155270560 4248485 0.027361819265674058 0.19143551723318455 chrY 59373566 247593 0.0041700880826325976 0.15632015322840875