BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173875.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,353,276 number of mapped reads = 1,316,763 (97.3%) number of supplementary alignments = 136,488 (10.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 659,882 number of mapped paired reads (second in pair) = 656,881 number of mapped paired reads (both in pair) = 1,293,814 number of mapped paired reads (singletons) = 22,949 number of mapped bases = 153,813,362 bp number of sequenced bases = 153,714,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 956,531 duplication rate = 60.49% >>>>>>> Insert size mean insert size = 1,049,074.2584 std insert size = 9,357,953.8835 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.889 >>>>>>> ACTG content number of A's = 46,640,428 bp (30.34%) number of C's = 29,772,490 bp (19.37%) number of T's = 46,481,341 bp (30.24%) number of G's = 30,818,189 bp (20.05%) number of N's = 1,617 bp (0%) GC percentage = 39.42% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 1,616,660 number of insertions = 19,138 mapped reads with insertion percentage = 1.39% number of deletions = 39,352 mapped reads with deletion percentage = 2.9% homopolymer indels = 41.46% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.9374X There is a 1.25% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 12262400 0.04919706900148506 0.767639519332722 chr2 243199373 13627276 0.05603335169782695 2.369582644774334 chr3 198022430 10666610 0.0538656656218187 0.6280870492583613 chr4 191154276 11053442 0.05782471745492107 0.8391228799956169 chr5 180915260 9252220 0.051141180683155193 0.6090591139582834 chr6 171115067 9363610 0.0547211310153068 0.6734740938552243 chr7 159138663 8685502 0.05457820140162922 0.7005110659310582 chr8 146364022 7827823 0.0534818795837682 0.859616994907462 chr9 141213431 6814446 0.0482563588445068 0.7048841441660315 chr10 135534747 7911157 0.05836995438520279 0.9653904941664445 chr11 135006516 6970540 0.05163113756672308 0.6280225219983878 chr12 133851895 7008741 0.05236191090159762 0.6114371508602914 chr13 115169878 5203877 0.04518435801416756 0.5807811766289387 chr14 107349540 4893756 0.045587116628538885 0.5789941683273214 chr15 102531392 4341361 0.04234177372721127 0.5509585522821213 chr16 90354753 4529357 0.050128596998101474 0.634818324186196 chr17 81195210 3821027 0.04705975882074817 0.5725170718293 chr18 78077248 4297680 0.05504394827030789 0.8574468438333482 chr19 59128983 2773281 0.04690222728843484 0.6594209679230432 chr20 63025520 3017522 0.047877780302328324 0.5993038484821194 chr21 48129895 2174769 0.0451854091931844 0.6466519360887575 chr22 51304566 1657303 0.032303226188483886 0.48042443655029504 chrMT 16571 239471 14.451209945084786 13.742254705443399 chrX 155270560 4142950 0.02668213472019422 0.43765990616883166 chrY 59373566 1277241 0.021511946915905304 0.60093922161212