BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173860.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,573,148 number of mapped reads = 5,422,037 (97.29%) number of supplementary alignments = 587,584 (10.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,714,550 number of mapped paired reads (second in pair) = 2,707,487 number of mapped paired reads (both in pair) = 5,319,308 number of mapped paired reads (singletons) = 102,729 number of mapped bases = 634,631,954 bp number of sequenced bases = 634,263,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,182,776 duplication rate = 64.22% >>>>>>> Insert size mean insert size = 926,639.0335 std insert size = 8,344,212.4874 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.5436 >>>>>>> ACTG content number of A's = 192,009,555 bp (30.27%) number of C's = 122,985,320 bp (19.39%) number of T's = 191,746,846 bp (30.23%) number of G's = 127,515,267 bp (20.1%) number of N's = 6,823 bp (0%) GC percentage = 39.49% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 6,419,313 number of insertions = 66,854 mapped reads with insertion percentage = 1.19% number of deletions = 147,406 mapped reads with deletion percentage = 2.65% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.205X std coverageData = 3.154X There is a 4.4% of reference with a coverageData >= 1X There is a 3.43% of reference with a coverageData >= 2X There is a 2.61% of reference with a coverageData >= 3X There is a 2.13% of reference with a coverageData >= 4X There is a 1.6% of reference with a coverageData >= 5X There is a 1.29% of reference with a coverageData >= 6X There is a 0.95% of reference with a coverageData >= 7X There is a 0.77% of reference with a coverageData >= 8X There is a 0.56% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 56467296 0.2265482660522639 1.8445088684769422 chr2 243199373 47403623 0.19491671551307824 9.296113618883183 chr3 198022430 39308813 0.1985068711660593 1.2871564382767355 chr4 191154276 40042921 0.20947959856257675 1.6678935171249374 chr5 180915260 31846994 0.17603265749942817 1.1832877606758005 chr6 171115067 31049435 0.1814535420191841 1.2630687392294102 chr7 159138663 55182074 0.3467546664005843 3.2423170596580695 chr8 146364022 63382605 0.433047713050684 2.358021809749541 chr9 141213431 21662459 0.15340225675842406 1.516437521878982 chr10 135534747 29165108 0.21518546826962387 4.120690600839018 chr11 135006516 26580854 0.19688571179779205 1.3378036852151083 chr12 133851895 24528303 0.18324957595856226 1.212197761721481 chr13 115169878 16926831 0.14697272667077063 1.0943366859876984 chr14 107349540 21500619 0.2002860841322655 1.2781233918418862 chr15 102531392 14947708 0.14578664844421502 1.0674033222500567 chr16 90354753 14861537 0.1644798586301265 1.556538776122655 chr17 81195210 15085908 0.18579800458672377 1.3693625817310044 chr18 78077248 12129628 0.1553541948609664 2.009523399936571 chr19 59128983 8205225 0.13876824162526186 1.350934997526816 chr20 63025520 23799994 0.3776247145600703 1.7584511042873066 chr21 48129895 7696986 0.15992110516758867 1.2769282878466257 chr22 51304566 6076656 0.11844279123226575 0.9283259280605267 chrMT 16571 1459199 88.05738941524349 63.66434344190742 chrX 155270560 24126895 0.15538615304794418 1.1223227244586935 chrY 59373566 1194283 0.020114725802388222 0.8492267556421155