BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716741.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 = 868,173 number of mapped reads = 682,898 (78.66%) number of supplementary alignments = 772 (0.09%) number of secondary alignments = 0 number of mapped bases = 35,828,973 bp number of sequenced bases = 35,820,903 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,009 duplication rate = 6.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1959 >>>>>>> ACTG content number of A's = 6,938,554 bp (19.37%) number of C's = 6,244,914 bp (17.43%) number of T's = 11,960,638 bp (33.39%) number of G's = 10,676,107 bp (29.8%) number of N's = 690 bp (0%) GC percentage = 47.24% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 230,272 number of insertions = 2,098 mapped reads with insertion percentage = 0.31% number of deletions = 4,810 mapped reads with deletion percentage = 0.7% homopolymer indels = 39.74% >>>>>>> Coverage mean coverageData = 0.0116X std coverageData = 0.1296X There is a 1.02% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 3480103 0.01396226411006615 0.1413760900878754 chr2 243199373 3123344 0.012842730478585567 0.17211804992858432 chr3 198022430 2392439 0.012081656608294323 0.12420582988403438 chr4 191154276 2212224 0.011572976792839309 0.122999938873753 chr5 180915260 2129838 0.01177257241871139 0.12209707245500032 chr6 171115067 1522072 0.008895020331552686 0.117110972645828 chr7 159138663 2034778 0.012786195143539694 0.1324019853384595 chr8 146364022 2100667 0.014352345414503573 0.1383674040037569 chr9 141213431 1617401 0.011453591832918499 0.12369566589510379 chr10 135534747 1857128 0.013702227960775254 0.14001708374625507 chr11 135006516 1573294 0.01165346715561492 0.1312206130136604 chr12 133851895 1708032 0.012760611271136655 0.12766501098998484 chr13 115169878 636540 0.005526966000606513 0.08525433837197681 chr14 107349540 1141235 0.010631019005763787 0.11707673100887103 chr15 102531392 711684 0.006941132721576627 0.09403680278634945 chr16 90354753 995934 0.011022486000266084 0.12176814928222283 chr17 81195210 1465812 0.01805293686659595 0.15757111058406376 chr18 78077248 973177 0.012464284089521188 0.13405923466391367 chr19 59128983 1013117 0.017134017001442424 0.16449816492174785 chr20 63025520 968181 0.015361729661254679 0.14668477007725894 chr21 48129895 512370 0.010645566544452258 0.12350888053212043 chr22 51304566 418455 0.008156291586210864 0.10400939719511498 chrMT 16571 3123 0.18846177056303182 0.5014272003528882 chrX 155270560 1145897 0.0073800017208671105 0.09787703177977097 chrY 59373566 92128 0.0015516669488910267 0.049115571560250336