BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524822.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 = 745,061 number of mapped reads = 671,359 (90.11%) number of supplementary alignments = 2,736 (0.37%) number of secondary alignments = 0 number of mapped bases = 38,494,584 bp number of sequenced bases = 38,481,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,567 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4275 >>>>>>> ACTG content number of A's = 9,896,252 bp (25.72%) number of C's = 6,535,407 bp (16.98%) number of T's = 12,399,762 bp (32.22%) number of G's = 9,649,731 bp (25.08%) number of N's = 713 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 199,490 number of insertions = 2,532 mapped reads with insertion percentage = 0.38% number of deletions = 7,954 mapped reads with deletion percentage = 1.18% homopolymer indels = 43.49% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 0.1501X There is a 1.18% of reference with a coverageData >= 1X There is a 0.05% 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 4043888 0.016224184251881966 0.24441172264516003 chr2 243199373 2963570 0.012185763324315807 0.1743592262282214 chr3 198022430 4040870 0.02040612268014285 0.14877138079966065 chr4 191154276 2080667 0.01088475258591652 0.1100067002236315 chr5 180915260 1661592 0.009184366205482058 0.09996414548697409 chr6 171115067 2298616 0.013433159570921945 0.12668987823774475 chr7 159138663 2501711 0.01572032184284469 0.23592093439834474 chr8 146364022 2417596 0.01651769312543215 0.16057306509464403 chr9 141213431 1147040 0.008122740109614644 0.10803960283390601 chr10 135534747 1899622 0.01401575641706108 0.1615989803785527 chr11 135006516 1625895 0.01204308538707865 0.12926286157782432 chr12 133851895 1456252 0.010879577013085994 0.10913579747029258 chr13 115169878 1141394 0.00991052538928625 0.10434376862591614 chr14 107349540 1622618 0.015115276693314196 0.12882241765387575 chr15 102531392 943776 0.0092047516530352 0.10091463733608526 chr16 90354753 1000101 0.011068604216094752 0.11542619453417167 chr17 81195210 678142 0.008351995148482281 0.09650485454679644 chr18 78077248 783431 0.01003404986815109 0.17700834265490714 chr19 59128983 609248 0.010303711802382936 0.17019121428749512 chr20 63025520 621157 0.009855642603186773 0.10398315969148834 chr21 48129895 454701 0.009447371534884919 0.10314542206344736 chr22 51304566 291296 0.005677779244833686 0.0779878854505948 chrMT 16571 52238 3.1523746303783717 2.4926745860179294 chrX 155270560 2057414 0.013250509304532681 0.12430336476812531 chrY 59373566 101749 0.0017137087571933948 0.05264551314533089