BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525104.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 = 2,655,370 number of mapped reads = 2,433,843 (91.66%) number of supplementary alignments = 12,363 (0.47%) number of secondary alignments = 0 number of mapped bases = 140,312,621 bp number of sequenced bases = 140,277,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,159 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3507 >>>>>>> ACTG content number of A's = 36,573,902 bp (26.07%) number of C's = 27,951,636 bp (19.93%) number of T's = 43,058,072 bp (30.69%) number of G's = 32,689,033 bp (23.3%) number of N's = 4,525 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 670,174 number of insertions = 7,629 mapped reads with insertion percentage = 0.31% number of deletions = 21,260 mapped reads with deletion percentage = 0.87% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0453X std coverageData = 0.3698X There is a 3.91% of reference with a coverageData >= 1X There is a 0.46% 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% 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 11241195 0.045099967875305715 0.6938914987824982 chr2 243199373 11955545 0.049159440061549826 0.3948645904375752 chr3 198022430 9487809 0.04791279957528043 0.24660485880092609 chr4 191154276 9219905 0.0482327949598156 0.276806258432578 chr5 180915260 8601084 0.04754205919390106 0.24786249432253593 chr6 171115067 8281092 0.04839487337488522 0.27665450115795154 chr7 159138663 7575408 0.04760256154722124 0.43321027223910596 chr8 146364022 7136428 0.04875807525977935 0.4045981567102598 chr9 141213431 5880622 0.04164350344267182 0.35458308075784734 chr10 135534747 6619500 0.0488398742501065 0.35382971737526087 chr11 135006516 6373202 0.04720662519726085 0.34519265591752585 chr12 133851895 6296820 0.04704318904114133 0.25432367637690323 chr13 115169878 4519929 0.03924575660312847 0.2213178491347131 chr14 107349540 4271772 0.03979310950005002 0.25505057299444517 chr15 102531392 3962306 0.03864480841145705 0.22175910681330635 chr16 90354753 3944984 0.04366105676809277 0.2616983052833 chr17 81195210 3696137 0.04552161389815976 0.25952270646941955 chr18 78077248 3792353 0.04857180673171267 0.6398861393126486 chr19 59128983 2755427 0.04660027722783597 0.5163451588063318 chr20 63025520 2976442 0.04722598084077688 0.2575566290914233 chr21 48129895 1887162 0.03920976765064624 0.25305281353721026 chr22 51304566 1581172 0.030819323176810423 0.19744393882809477 chrMT 16571 8734 0.527065355138495 0.8135842526285759 chrX 155270560 7844168 0.0505193515113232 0.2918407337340956 chrY 59373566 403425 0.006794690418291534 0.162067079434297