BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716298.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 = 983,283 number of mapped reads = 822,471 (83.65%) number of supplementary alignments = 3,363 (0.34%) number of secondary alignments = 0 number of mapped bases = 48,092,222 bp number of sequenced bases = 48,077,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,992 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3723 >>>>>>> ACTG content number of A's = 12,075,934 bp (25.12%) number of C's = 9,099,684 bp (18.93%) number of T's = 15,295,267 bp (31.81%) number of G's = 11,605,750 bp (24.14%) number of N's = 1,323 bp (0%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 236,916 number of insertions = 3,647 mapped reads with insertion percentage = 0.44% number of deletions = 9,075 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.14% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 0.166X There is a 1.45% of reference with a coverageData >= 1X There is a 0.08% 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 3914658 0.015705710117368172 0.2783534248285375 chr2 243199373 4039601 0.01661024430354925 0.19840850629228562 chr3 198022430 3185149 0.016084788980723044 0.13410843071128797 chr4 191154276 3083516 0.016131033343978137 0.1396451623754825 chr5 180915260 2856224 0.01578763449805174 0.13337474227037358 chr6 171115067 2825933 0.016514811054014315 0.15093110121474868 chr7 159138663 2676192 0.016816730450977837 0.18342454360887564 chr8 146364022 2427063 0.01658237432147089 0.15592026841803164 chr9 141213431 1983196 0.01404396158322929 0.14345851367038426 chr10 135534747 2319428 0.017113161394693863 0.16612363876399014 chr11 135006516 2184028 0.01617720436545448 0.15058909874625412 chr12 133851895 2185312 0.01632634338124238 0.13664580032882082 chr13 115169878 1503466 0.013054333529814107 0.12154381861702997 chr14 107349540 1462633 0.013624958243882554 0.12618418286962094 chr15 102531392 1394763 0.013603277716155458 0.12419671337333876 chr16 90354753 1400765 0.015502947587051674 0.13582572956682695 chr17 81195210 1294716 0.015945718965441433 0.1374247446517842 chr18 78077248 1256915 0.016098351724691935 0.21829964195839552 chr19 59128983 999855 0.016909727671115194 0.21026509402120527 chr20 63025520 1024225 0.016250956755295316 0.1366267929976621 chr21 48129895 637488 0.01324515667445358 0.1296272755322105 chr22 51304566 579080 0.011287104543482543 0.11220819000074891 chrMT 16571 3606 0.2176090760967956 0.4696639797910404 chrX 155270560 2705886 0.017426909518456043 0.14690869296051884 chrY 59373566 148524 0.0025015172576968005 0.07553789064584536