BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716348.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 = 624,099 number of mapped reads = 584,120 (93.59%) number of supplementary alignments = 12,343 (1.98%) number of secondary alignments = 0 number of mapped bases = 45,903,748 bp number of sequenced bases = 45,882,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,892 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3334 >>>>>>> ACTG content number of A's = 11,808,721 bp (25.74%) number of C's = 9,206,991 bp (20.07%) number of T's = 13,866,522 bp (30.22%) number of G's = 10,996,369 bp (23.97%) number of N's = 3,514 bp (0.01%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 291,823 number of insertions = 3,641 mapped reads with insertion percentage = 0.61% number of deletions = 11,295 mapped reads with deletion percentage = 1.9% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1648X There is a 1.39% of reference with a coverageData >= 1X There is a 0.06% 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 3701609 0.014850951966133718 0.27685357116554354 chr2 243199373 3866165 0.015897101017608297 0.18172471500399326 chr3 198022430 3033148 0.015317194117858264 0.12826810584507997 chr4 191154276 2987050 0.015626383372140732 0.14401088794107714 chr5 180915260 2788823 0.015415078860677646 0.1295598802419316 chr6 171115067 2616573 0.015291306872468454 0.1330475120112887 chr7 159138663 2505810 0.01574607925416591 0.19765542761332666 chr8 146364022 2325742 0.015890120865905147 0.18533351733628334 chr9 141213431 1916978 0.013575040181553269 0.1539054194654872 chr10 135534747 2214627 0.016339920566642588 0.17764121123636883 chr11 135006516 2105499 0.015595536144344321 0.15334359712422538 chr12 133851895 2084064 0.015569925252085523 0.13014148464856337 chr13 115169878 1436337 0.012471464109738832 0.1157951846662375 chr14 107349540 1394659 0.012991755716885232 0.12375088846615964 chr15 102531392 1344444 0.01311251094689127 0.11900387539111187 chr16 90354753 1344022 0.01487494520625827 0.13174691567676963 chr17 81195210 1231168 0.015163061958950534 0.13343900769458975 chr18 78077248 1226282 0.015706009515089468 0.2090885052180213 chr19 59128983 905787 0.015318832728782093 0.1903579069916455 chr20 63025520 992795 0.015752269874171606 0.13318893115935448 chr21 48129895 610941 0.012693586802963107 0.12647436897154413 chr22 51304566 540654 0.010538126372611747 0.10656697209779188 chrMT 16571 7637 0.4608653672077726 0.6924341183633828 chrX 155270560 2579356 0.016612009385423742 0.14216654096017473 chrY 59373566 143578 0.002418214193164682 0.08773769492284283