BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716497.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 = 1,261,388 number of mapped reads = 1,149,845 (91.16%) number of supplementary alignments = 5,606 (0.44%) number of secondary alignments = 0 number of mapped bases = 67,101,157 bp number of sequenced bases = 67,081,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,183 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0389 >>>>>>> ACTG content number of A's = 17,823,573 bp (26.57%) number of C's = 12,587,799 bp (18.76%) number of T's = 20,434,007 bp (30.46%) number of G's = 16,234,610 bp (24.2%) number of N's = 1,701 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 336,783 number of insertions = 5,615 mapped reads with insertion percentage = 0.49% number of deletions = 12,352 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.0217X std coverageData = 0.2418X There is a 1.94% of reference with a coverageData >= 1X There is a 0.17% 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 6317875 0.025347479475286844 0.5054619163070029 chr2 243199373 6416850 0.02638514203735221 0.2861913876795053 chr3 198022430 4615821 0.023309586696820154 0.16610870791679558 chr4 191154276 3161052 0.016536653357416917 0.1610895855536509 chr5 180915260 2927129 0.01617955831918214 0.14046828719201887 chr6 171115067 4586263 0.02680221607837725 0.19373091784748525 chr7 159138663 4888000 0.030715351680439845 0.30943687387105434 chr8 146364022 3869166 0.02643522600110019 0.21538019605171488 chr9 141213431 2819225 0.0199642837089625 0.18959648690417732 chr10 135534747 3772517 0.027834316169860117 0.23172280164634015 chr11 135006516 2235361 0.016557430457652872 0.17818042774901519 chr12 133851895 2706113 0.020217218441322776 0.15870220439515395 chr13 115169878 1493022 0.012963650096078073 0.12503854803403172 chr14 107349540 1499105 0.013964708185987568 0.1366641921253501 chr15 102531392 1400246 0.013656754021246487 0.12863531643766707 chr16 90354753 1442625 0.01596623256775435 0.14449988053921525 chr17 81195210 1507476 0.018566070584705673 0.15382755135441892 chr18 78077248 2342173 0.029998150037255412 0.32478725697843314 chr19 59128983 1668185 0.028212644888548143 0.3107647739590928 chr20 63025520 1068075 0.016946706667394413 0.1440702332945654 chr21 48129895 859673 0.017861518293360083 0.16062018778024706 chr22 51304566 865052 0.016861111348256994 0.14165458441827733 chrMT 16571 112864 6.810934765554282 4.514660359686055 chrX 155270560 4341983 0.027963981066339943 0.20259671019449757 chrY 59373566 185306 0.003121018535420291 0.09546168852299881