BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716788.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 = 3,453,074 number of mapped reads = 3,137,344 (90.86%) number of supplementary alignments = 67,871 (1.97%) number of secondary alignments = 0 number of mapped bases = 233,060,981 bp number of sequenced bases = 232,981,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,536 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2853 >>>>>>> ACTG content number of A's = 61,560,405 bp (26.42%) number of C's = 48,538,508 bp (20.83%) number of T's = 69,037,373 bp (29.63%) number of G's = 53,818,183 bp (23.1%) number of N's = 26,898 bp (0.01%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,748,232 number of insertions = 20,008 mapped reads with insertion percentage = 0.63% number of deletions = 46,756 mapped reads with deletion percentage = 1.47% homopolymer indels = 39.53% >>>>>>> Coverage mean coverageData = 0.0753X std coverageData = 0.5449X There is a 5.91% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18069192 0.07249407013513519 0.6280101141662078 chr2 243199373 19734610 0.08114580953298757 0.7855498533625683 chr3 198022430 15256278 0.07704318142141776 0.3385100787528928 chr4 191154276 14873090 0.07780673449334714 0.3834809094792317 chr5 180915260 13623420 0.0753027688211597 0.343067548980786 chr6 171115067 13457316 0.07864483377141769 0.4016222072685705 chr7 159138663 12464217 0.07832299684458201 0.7303516012097078 chr8 146364022 11626624 0.07943635219316397 0.7290207499692138 chr9 141213431 9592297 0.0679276534255442 0.5988165436722607 chr10 135534747 11274227 0.08318329616242247 0.5626507065955664 chr11 135006516 10055853 0.07448420489571037 0.5830635185717202 chr12 133851895 10213219 0.0763023863054012 0.3509754942601999 chr13 115169878 7461835 0.06478981422555645 0.30983837316962964 chr14 107349540 6932449 0.06457828324182852 0.40053147671757067 chr15 102531392 6767769 0.06600679916644456 0.31665693262343725 chr16 90354753 6833412 0.07562869437538056 0.3916256643714921 chr17 81195210 6198411 0.07633961412255723 0.3971917217821944 chr18 78077248 6428001 0.08232873422997695 1.1689026851053457 chr19 59128983 4493922 0.07600201748776907 0.5374316758045715 chr20 63025520 4918250 0.07803584960504888 0.3690925749181179 chr21 48129895 2991586 0.062156503769642546 0.34739435141417335 chr22 51304566 2554834 0.0497974000988528 0.271059137129122 chrMT 16571 52077 3.142658861867117 3.465920647504233 chrX 155270560 16521562 0.10640498752628959 0.5095306246398842 chrY 59373566 666530 0.011226039547633033 0.26762964057034916