BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819077.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,803,658 number of mapped reads = 1,627,878 (90.25%) number of supplementary alignments = 6,168 (0.34%) number of secondary alignments = 0 number of mapped bases = 93,286,000 bp number of sequenced bases = 93,257,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,699 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8204 >>>>>>> ACTG content number of A's = 23,398,643 bp (25.09%) number of C's = 17,405,490 bp (18.66%) number of T's = 29,949,582 bp (32.12%) number of G's = 22,502,067 bp (24.13%) number of N's = 1,297 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 477,883 number of insertions = 7,269 mapped reads with insertion percentage = 0.44% number of deletions = 17,631 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.94% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2721X There is a 2.7% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 9276977 0.03721947396873286 0.47878369879635857 chr2 243199373 7374617 0.030323338868147493 0.3210642336694258 chr3 198022430 5119502 0.025853141990026078 0.17828512762830198 chr4 191154276 5171288 0.02705295486039768 0.20408663596550858 chr5 180915260 5111780 0.028255106838417057 0.1852123745507109 chr6 171115067 4037360 0.023594415563651095 0.21112269376503726 chr7 159138663 4706533 0.029575044249303514 0.33970550781131326 chr8 146364022 7584298 0.05181804856387453 0.28991704879451335 chr9 141213431 4387109 0.031067221927353356 0.24685490766633014 chr10 135534747 4866086 0.03590286703379466 0.2883501893946303 chr11 135006516 3272348 0.024238444905874023 0.2621338276703973 chr12 133851895 4403676 0.03289961640064939 0.1992119356726159 chr13 115169878 2072512 0.017995260878890574 0.1463586764934752 chr14 107349540 2251670 0.02097512481189952 0.16328150739872796 chr15 102531392 2479788 0.024185646479860528 0.1806352171674349 chr16 90354753 2958471 0.03274283755720078 0.21389168904164033 chr17 81195210 3352242 0.041286203952178954 0.23307557550423028 chr18 78077248 2210415 0.02831061617335693 0.41664739017711955 chr19 59128983 1983348 0.03354273825409783 0.3381605170848374 chr20 63025520 2673636 0.042421482599429565 0.2274682083290159 chr21 48129895 1266523 0.02631468445962743 0.19053253784632596 chr22 51304566 796831 0.01553138564703968 0.13509965648864294 chrMT 16571 2370 0.14302094019672923 0.373447371897565 chrX 155270560 5617864 0.03618112796141136 0.23816169001196483 chrY 59373566 308756 0.005200226646315972 0.14396524876406758