BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716479.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 = 1,509,986 number of mapped reads = 1,345,840 (89.13%) number of supplementary alignments = 5,104 (0.34%) number of secondary alignments = 0 number of mapped bases = 76,644,836 bp number of sequenced bases = 76,621,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,776 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2973 >>>>>>> ACTG content number of A's = 18,248,405 bp (23.82%) number of C's = 15,538,773 bp (20.28%) number of T's = 23,441,398 bp (30.59%) number of G's = 19,392,547 bp (25.31%) number of N's = 543 bp (0%) GC percentage = 45.59% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 403,098 number of insertions = 4,449 mapped reads with insertion percentage = 0.33% number of deletions = 14,452 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2159X There is a 2.27% of reference with a coverageData >= 1X There is a 0.15% 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 6575959 0.02638291922249614 0.2789613350782341 chr2 243199373 6130644 0.02520830512174059 0.2958380264101815 chr3 198022430 4495313 0.022701029373288672 0.16418286177907607 chr4 191154276 4752139 0.024860228604041273 0.17886789957821392 chr5 180915260 4434032 0.024508888857689506 0.16665700504898173 chr6 171115067 4188118 0.024475448441953974 0.19232235365634248 chr7 159138663 4451421 0.027971964298832898 0.3043004594720552 chr8 146364022 4030369 0.027536610055714374 0.2147675020469415 chr9 141213431 2595989 0.01838344257778143 0.1684662200792919 chr10 135534747 3450202 0.025456217511513855 0.26800792255964434 chr11 135006516 2754773 0.020404741057090902 0.1846877735479996 chr12 133851895 3895472 0.029102852821022818 0.1835414847228176 chr13 115169878 2334511 0.020270152582778634 0.15250593154022435 chr14 107349540 2622272 0.02442741720178773 0.17224484823325814 chr15 102531392 2875827 0.028048258625026763 0.18170144755898085 chr16 90354753 2685464 0.029721336297604622 0.19490044311097016 chr17 81195210 3491153 0.042997031475132584 0.23210049921423337 chr18 78077248 1468425 0.018807335524940634 0.2566022934909586 chr19 59128983 1771299 0.029956527410593212 0.2637652187047482 chr20 63025520 1455064 0.02308690194067419 0.16520154673200707 chr21 48129895 971143 0.020177542460875927 0.16094856453329848 chr22 51304566 731228 0.01425268854238042 0.12854386185845643 chrMT 16571 24684 1.4895902480236558 1.6403945403036704 chrX 155270560 4228407 0.02723250949825904 0.18616783688413713 chrY 59373566 230928 0.0038894076195457082 0.11071110645432129