BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013221.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,771,986 number of mapped reads = 1,549,852 (87.46%) number of supplementary alignments = 13,788 (0.78%) number of secondary alignments = 0 number of mapped bases = 100,970,719 bp number of sequenced bases = 100,917,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,860 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0091 >>>>>>> ACTG content number of A's = 27,558,597 bp (27.31%) number of C's = 18,157,265 bp (17.99%) number of T's = 32,639,930 bp (32.34%) number of G's = 22,559,935 bp (22.35%) number of N's = 1,432 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 770,748 number of insertions = 7,409 mapped reads with insertion percentage = 0.48% number of deletions = 31,418 mapped reads with deletion percentage = 2% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.2952X There is a 2.58% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 5126400 0.02056725066293817 0.2799642935380857 chr2 243199373 9153750 0.037638871708768756 0.4091949396195109 chr3 198022430 6967908 0.035187468409513006 0.22812210437542696 chr4 191154276 6003618 0.03140718651776327 0.22412196072081428 chr5 180915260 2477521 0.013694372713501338 0.1456737920637185 chr6 171115067 4886882 0.028559039748381712 0.2427115863642229 chr7 159138663 7444315 0.046778795672048595 0.46020190546443784 chr8 146364022 6673718 0.04559671091847968 0.4308309985044889 chr9 141213431 3830188 0.02712339734879751 0.2770850242906481 chr10 135534747 4374030 0.03227238842302188 0.3340914346813363 chr11 135006516 1585231 0.011741885110197199 0.16958391761544106 chr12 133851895 4892751 0.03655346829419188 0.234749398329258 chr13 115169878 1457112 0.012651849817883804 0.13716898011636416 chr14 107349540 4343408 0.04046042488863948 0.25134015266548126 chr15 102531392 3125015 0.03047861673427783 0.21040195336279463 chr16 90354753 5656039 0.06259813471019061 0.3167289757604323 chr17 81195210 5081529 0.06258409824914549 0.3609141014114368 chr18 78077248 3412742 0.04370981415738424 0.4520007490834223 chr19 59128983 2342766 0.03962128014276856 0.37343173883918457 chr20 63025520 2073843 0.03290481379606229 0.22475628653966714 chr21 48129895 2597565 0.05396988711485865 0.29511416566779686 chr22 51304566 1458667 0.028431524008993663 0.20167308961123923 chrMT 16571 13296 0.8023655784201316 1.2187853806060727 chrX 155270560 5802267 0.03736875168093681 0.24982268940620717 chrY 59373566 190158 0.0032027384038209867 0.0936761347766437