BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008752.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 = 1,590,550 number of mapped reads = 1,170,177 (73.57%) number of supplementary alignments = 5,360 (0.34%) number of secondary alignments = 0 number of mapped bases = 77,712,792 bp number of sequenced bases = 77,665,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,265 duplication rate = 2.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.5982 >>>>>>> ACTG content number of A's = 24,586,401 bp (31.66%) number of C's = 13,220,603 bp (17.02%) number of T's = 22,836,910 bp (29.4%) number of G's = 17,006,762 bp (21.9%) number of N's = 14,733 bp (0.02%) GC percentage = 38.92% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 896,428 number of insertions = 6,204 mapped reads with insertion percentage = 0.53% number of deletions = 31,414 mapped reads with deletion percentage = 2.65% homopolymer indels = 49.83% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2128X There is a 2.12% of reference with a coverageData >= 1X There is a 0.28% 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% 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 5920677 0.023753910727468158 0.23799748376750654 chr2 243199373 6991696 0.02874882411806218 0.24897935857925677 chr3 198022430 6162669 0.031121065426780187 0.20835909611037595 chr4 191154276 4212635 0.02203788002105692 0.17552925900944458 chr5 180915260 4203037 0.02323207561374314 0.17878008296691136 chr6 171115067 4250846 0.024842032174758756 0.1986293896809501 chr7 159138663 4449811 0.02796184733561573 0.26118877957983194 chr8 146364022 6453408 0.044091491281921726 0.31934535776507134 chr9 141213431 2651990 0.018780012504617923 0.18820625948242967 chr10 135534747 4154424 0.0306520954364566 0.22558886480707702 chr11 135006516 3517834 0.026056771956103213 0.21488261995663907 chr12 133851895 3506267 0.02619512409592707 0.19117225015595046 chr13 115169878 2422484 0.021034006825986218 0.17080991168053547 chr14 107349540 2813992 0.026213358715836136 0.19326334428593045 chr15 102531392 2169796 0.02116226023733297 0.1723951755269656 chr16 90354753 1908100 0.02111787079977962 0.17494658769036608 chr17 81195210 1904415 0.0234547702998736 0.19848948077589904 chr18 78077248 1512125 0.019367037629195127 0.2806330963685082 chr19 59128983 1187447 0.02008231732989556 0.17827153555682665 chr20 63025520 1702905 0.027019293137129214 0.19195253305378487 chr21 48129895 855960 0.01778437289339609 0.16132869090152788 chr22 51304566 829789 0.016173784610126123 0.14894632665313226 chrMT 16571 25330 1.5285740148452116 2.021520428226816 chrX 155270560 3749894 0.024150708286232753 0.18836728533538563 chrY 59373566 155261 0.0026149852612861423 0.06524779596805598