BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524303.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 = 2,448,877 number of mapped reads = 2,241,756 (91.54%) number of supplementary alignments = 9,339 (0.38%) number of secondary alignments = 0 number of mapped bases = 130,827,472 bp number of sequenced bases = 130,790,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,927 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3667 >>>>>>> ACTG content number of A's = 32,030,751 bp (24.49%) number of C's = 22,702,705 bp (17.36%) number of T's = 41,703,920 bp (31.89%) number of G's = 34,334,365 bp (26.25%) number of N's = 18,684 bp (0.01%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 668,955 number of insertions = 9,068 mapped reads with insertion percentage = 0.4% number of deletions = 23,481 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.3777X There is a 3.71% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10912107 0.04377965822600699 0.753516927386836 chr2 243199373 8512329 0.035001443034147955 0.5084189850886252 chr3 198022430 9061044 0.04575766492714992 0.2370299515703743 chr4 191154276 6869901 0.03593903910368189 0.24533670037396832 chr5 180915260 7633368 0.0421930576779427 0.22827249354489856 chr6 171115067 8412703 0.04916401078813241 0.27447112939415524 chr7 159138663 5960087 0.03745216208081376 0.4695896150540735 chr8 146364022 13701081 0.09360962354532729 0.46070808017595555 chr9 141213431 5405248 0.03827715226322913 0.27889709411898606 chr10 135534747 6698034 0.04941931237751158 0.3611879499076696 chr11 135006516 6181541 0.0457869826075654 0.2998222377490759 chr12 133851895 5186714 0.03874964937926355 0.22239028792256071 chr13 115169878 3334721 0.028954801879706775 0.190087682234031 chr14 107349540 2764041 0.02574804698743935 0.19041623822955772 chr15 102531392 4054479 0.039543781869264 0.22198347424492262 chr16 90354753 4153048 0.04596380225841578 0.26168936950485117 chr17 81195210 4116153 0.05069452988667681 0.27991851498994125 chr18 78077248 3026005 0.03875655299735974 0.5101249171356058 chr19 59128983 2368263 0.04005248999462751 0.4570220622418194 chr20 63025520 3001607 0.0476252635440374 0.24929283299529936 chr21 48129895 1877923 0.039017807954910354 0.24556911868506576 chr22 51304566 993473 0.01936422189011403 0.15440625945174136 chrMT 16571 5455 0.3291895480055519 0.6528728016665867 chrX 155270560 6233402 0.040145420999318865 0.25479839968031226 chrY 59373566 364745 0.0061432220527229235 0.17100236407559707