BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525111.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 = 2,080,209 number of mapped reads = 1,876,714 (90.22%) number of supplementary alignments = 59,054 (2.84%) number of secondary alignments = 0 number of mapped bases = 144,224,459 bp number of sequenced bases = 144,164,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,529 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4303 >>>>>>> ACTG content number of A's = 37,224,290 bp (25.82%) number of C's = 28,174,641 bp (19.54%) number of T's = 44,327,209 bp (30.75%) number of G's = 34,432,377 bp (23.88%) number of N's = 5,775 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,093,862 number of insertions = 11,881 mapped reads with insertion percentage = 0.62% number of deletions = 34,468 mapped reads with deletion percentage = 1.81% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.4835X There is a 4.04% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 13980332 0.05608945704492347 0.8925733712159039 chr2 243199373 11912281 0.048981544866071675 0.6645197226749341 chr3 198022430 8992987 0.04541398163834268 0.23795687991260478 chr4 191154276 8951202 0.046827108382341394 0.2594874698101006 chr5 180915260 8373311 0.04628305539289499 0.24378270949272235 chr6 171115067 7729090 0.045168962239894396 0.2677795766789242 chr7 159138663 7875073 0.04948560489037161 0.6716332579241627 chr8 146364022 7131874 0.048726961056044224 0.6028561719192944 chr9 141213431 5869983 0.04156816358353335 0.42968362524163595 chr10 135534747 6616131 0.04881501715571137 0.4598112035185852 chr11 135006516 7877758 0.058350946557275796 0.5727254140077956 chr12 133851895 6353701 0.04746814380177434 0.24395210499348796 chr13 115169878 5128288 0.044528031886948774 0.2355761877122472 chr14 107349540 4220384 0.03931441159412514 0.26496291040675424 chr15 102531392 4006947 0.0390801970190749 0.22101918880031782 chr16 90354753 3329897 0.036853589760795426 0.2539563935961331 chr17 81195210 4503818 0.055469011041414884 0.3353400105291897 chr18 78077248 3820237 0.04892894022084385 0.8069091165822793 chr19 59128983 2929680 0.04954727531843394 0.6499765459915923 chr20 63025520 2862570 0.04541922065855228 0.24792386315861897 chr21 48129895 1879242 0.039045212959637664 0.2409422226242442 chr22 51304566 1591831 0.03102708246279678 0.1947298218288444 chrMT 16571 1898 0.1145374449339207 0.3605867533358313 chrX 155270560 7935830 0.05110968879097235 0.34948212011930785 chrY 59373566 350114 0.005896799259118107 0.13540052367009853