BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867856.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 = 690,530 number of mapped reads = 612,122 (88.65%) number of supplementary alignments = 3,281 (0.48%) number of secondary alignments = 0 number of mapped bases = 35,974,896 bp number of sequenced bases = 35,964,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,064 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.953 >>>>>>> ACTG content number of A's = 9,353,941 bp (26.01%) number of C's = 6,649,717 bp (18.49%) number of T's = 10,872,886 bp (30.23%) number of G's = 9,083,041 bp (25.26%) number of N's = 5,195 bp (0.01%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 208,011 number of insertions = 3,103 mapped reads with insertion percentage = 0.5% number of deletions = 6,153 mapped reads with deletion percentage = 0.99% homopolymer indels = 40.7% >>>>>>> Coverage mean coverageData = 0.0116X std coverageData = 0.2451X There is a 1.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2907151 0.01166356572487737 0.5490044843109134 chr2 243199373 3006790 0.012363477598274894 0.2538220347934031 chr3 198022430 2291222 0.011570517541876444 0.11887616828798515 chr4 191154276 2323214 0.01215360727792456 0.1408458239822654 chr5 180915260 2131242 0.011780332958093198 0.11802555424491232 chr6 171115067 2002547 0.011702926195271864 0.13582092250018077 chr7 159138663 2062473 0.012960225762359208 0.3111944042428147 chr8 146364022 1823392 0.012457924940051183 0.23892796615999407 chr9 141213431 1497419 0.010603941773782127 0.19553064109366267 chr10 135534747 1857603 0.013705732597117697 0.2746430277963956 chr11 135006516 1643443 0.012173064298615038 0.18218694918909217 chr12 133851895 1607423 0.012008967075139279 0.11980868613339493 chr13 115169878 1020587 0.008861579240363526 0.0984987709506122 chr14 107349540 1061945 0.009892403823994029 0.1285829282616985 chr15 102531392 955859 0.009322598487690481 0.1106625230111474 chr16 90354753 1063564 0.011770980105495944 0.14430536205928923 chr17 81195210 1005335 0.012381703304911706 0.13061526698440798 chr18 78077248 954993 0.01223138653657465 0.4016257707884608 chr19 59128983 874549 0.01479053005190365 0.4040441753640854 chr20 63025520 700441 0.011113609217345609 0.11458681719248265 chr21 48129895 452729 0.009406399078992381 0.12909461472283015 chr22 51304566 407535 0.00794344503372273 0.09251466191939958 chrMT 16571 7189 0.433830185263412 0.6977673890300103 chrX 155270560 2116555 0.013631399281357651 0.15049521207147595 chrY 59373566 199696 0.003363382283624332 0.17482486727967636