BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524290.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 = 1,153,462 number of mapped reads = 1,065,236 (92.35%) number of supplementary alignments = 4,003 (0.35%) number of secondary alignments = 0 number of mapped bases = 62,689,100 bp number of sequenced bases = 62,669,525 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,451 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4014 >>>>>>> ACTG content number of A's = 15,899,886 bp (25.37%) number of C's = 11,569,106 bp (18.46%) number of T's = 20,246,502 bp (32.31%) number of G's = 14,945,590 bp (23.85%) number of N's = 8,441 bp (0.01%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 308,797 number of insertions = 4,317 mapped reads with insertion percentage = 0.4% number of deletions = 12,255 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.2193X There is a 1.87% of reference with a coverageData >= 1X There is a 0.1% 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 4922108 0.019747625824370563 0.4078357099808541 chr2 243199373 5337791 0.021948210368124593 0.22910473946389653 chr3 198022430 4248451 0.021454392818025716 0.15453735184149928 chr4 191154276 4152342 0.021722464633749546 0.16602944090635652 chr5 180915260 3799039 0.02099899698897705 0.15368275138834264 chr6 171115067 3645657 0.02130529510881704 0.16308602474573877 chr7 159138663 3410764 0.021432654615176704 0.28852204869993786 chr8 146364022 3324863 0.0227163954267395 0.2116043762758846 chr9 141213431 2640225 0.01869669889969602 0.19434041636794738 chr10 135534747 3025169 0.022320246777750654 0.21051783100160792 chr11 135006516 2887124 0.021385071517585123 0.2042134961311388 chr12 133851895 2844646 0.021252190714221863 0.1577887244902298 chr13 115169878 1775856 0.015419448477665314 0.13118666646326502 chr14 107349540 1911681 0.017808003648641626 0.14801193277936966 chr15 102531392 1788833 0.017446685986668355 0.140223693362552 chr16 90354753 1791858 0.0198313640456745 0.16181817452432679 chr17 81195210 1652293 0.020349636388649034 0.16109080086509822 chr18 78077248 1718907 0.022015466016425168 0.3728812228337915 chr19 59128983 1203676 0.020356785098096478 0.2943526774555378 chr20 63025520 1313140 0.020835052213769915 0.15440132394768744 chr21 48129895 830465 0.017254660538943624 0.15313748813971384 chr22 51304566 704019 0.013722345882430815 0.12307599095443669 chrMT 16571 9783 0.5903687164323215 0.813834828786783 chrX 155270560 3562620 0.022944594261784076 0.1784533220137527 chrY 59373566 187790 0.003162855335318751 0.09472350497926697