BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237611.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 = 1,651,360 number of mapped reads = 1,461,306 (88.49%) number of supplementary alignments = 7,126 (0.43%) number of secondary alignments = 0 number of mapped bases = 94,863,099 bp number of sequenced bases = 94,818,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,065 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2606 >>>>>>> ACTG content number of A's = 25,162,856 bp (26.54%) number of C's = 16,886,848 bp (17.81%) number of T's = 30,458,964 bp (32.12%) number of G's = 22,155,453 bp (23.37%) number of N's = 154,712 bp (0.16%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 810,934 number of insertions = 8,689 mapped reads with insertion percentage = 0.59% number of deletions = 26,681 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.3678X There is a 2.74% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 10048641 0.04031541008678169 0.6630475457759907 chr2 243199373 8055547 0.03312322273133492 0.5796586475816113 chr3 198022430 5264095 0.02658332694937639 0.18381535621290923 chr4 191154276 5571619 0.02914723707253088 0.20219802107967821 chr5 180915260 5112493 0.028259047910054687 0.1850445628220376 chr6 171115067 5150098 0.030097279510751675 0.2664301736131621 chr7 159138663 5967949 0.037501565537219575 0.5825983723326056 chr8 146364022 5205406 0.03556479200879025 0.39669482240822546 chr9 141213431 3691773 0.026143214380224215 0.2930718974521555 chr10 135534747 4053168 0.02990501026279261 0.35000852530788773 chr11 135006516 4112357 0.030460433480114398 0.2809270426707334 chr12 133851895 3892897 0.02908361514045057 0.18929116825025552 chr13 115169878 3442542 0.0298909928514468 0.19495044203175307 chr14 107349540 2239138 0.02085838467495995 0.1785745647987983 chr15 102531392 3168590 0.03090360852606 0.19859202586582683 chr16 90354753 2419800 0.026781103590643427 0.22483743511877008 chr17 81195210 2980784 0.03671132816825032 0.23498193084157273 chr18 78077248 2269352 0.029065471160049084 0.5762167922587013 chr19 59128983 2071449 0.035032718218745616 0.4235049388957584 chr20 63025520 1758478 0.027901047067917885 0.19674678189872188 chr21 48129895 1465646 0.030451884426508723 0.20994524146931423 chr22 51304566 1108638 0.0216089538697199 0.15903953712111535 chrMT 16571 43038 2.5971878583066803 2.5079825587838225 chrX 155270560 5481016 0.03529977608118371 0.23719274938846843 chrY 59373566 288585 0.004860496336029404 0.13418499610920118