BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717048.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 = 1,060,950 number of mapped reads = 899,142 (84.75%) number of supplementary alignments = 3,375 (0.32%) number of secondary alignments = 0 number of mapped bases = 50,425,176 bp number of sequenced bases = 50,410,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,267 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2978 >>>>>>> ACTG content number of A's = 11,695,982 bp (23.2%) number of C's = 10,870,820 bp (21.56%) number of T's = 14,653,448 bp (29.07%) number of G's = 13,188,529 bp (26.16%) number of N's = 1,525 bp (0%) GC percentage = 47.73% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 263,868 number of insertions = 3,172 mapped reads with insertion percentage = 0.35% number of deletions = 8,482 mapped reads with deletion percentage = 0.93% homopolymer indels = 35.17% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1581X There is a 1.49% of reference with a coverageData >= 1X There is a 0.1% 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 4897075 0.019647192774697238 0.19148571237916204 chr2 243199373 4316112 0.01774721680717491 0.18688293281356447 chr3 198022430 3344184 0.016887905072167836 0.1441425781781332 chr4 191154276 3231828 0.016906909265268017 0.15624836524994404 chr5 180915260 3062762 0.01692926290463281 0.1402985075121688 chr6 171115067 2223628 0.012994928143878762 0.12513318016191546 chr7 159138663 2936795 0.018454314901464267 0.17393274761622576 chr8 146364022 3052409 0.0208549133748183 0.16379746324293526 chr9 141213431 2174701 0.015400100292159886 0.14644517175049324 chr10 135534747 2685617 0.01981497040017347 0.23455255793007454 chr11 135006516 2051128 0.015192807434568566 0.1577896489136514 chr12 133851895 2433910 0.01818360509576648 0.1464587703149921 chr13 115169878 903074 0.007841234319966892 0.09570427258064057 chr14 107349540 1579935 0.01471766902773873 0.13633605858961528 chr15 102531392 981005 0.009567850205330285 0.10759877450663308 chr16 90354753 1397193 0.015463414525630987 0.14303241057310448 chr17 81195210 2046994 0.025210772901504905 0.17967040763595293 chr18 78077248 1354946 0.017353915957693592 0.17175390233138857 chr19 59128983 1420123 0.024017375708964925 0.19335216729115787 chr20 63025520 1303224 0.020677719120762512 0.16247134501136437 chr21 48129895 703205 0.014610565844783164 0.14522160727417377 chr22 51304566 577902 0.011264143624175672 0.11695292678655989 chrMT 16571 1448 0.08738157021302274 0.3284318016473525 chrX 155270560 1585806 0.01021317885373763 0.11691350232512711 chrY 59373566 160172 0.002697698837896986 0.08946474725032001