BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174020.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 = 5,945,348 number of mapped reads = 5,786,681 (97.33%) number of supplementary alignments = 557,994 (9.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,897,814 number of mapped paired reads (second in pair) = 2,888,867 number of mapped paired reads (both in pair) = 5,681,294 number of mapped paired reads (singletons) = 105,387 number of mapped bases = 682,089,375 bp number of sequenced bases = 681,719,029 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,495,519 duplication rate = 65.5% >>>>>>> Insert size mean insert size = 890,214.8969 std insert size = 8,178,080.1973 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.7207 >>>>>>> ACTG content number of A's = 206,880,364 bp (30.35%) number of C's = 132,188,551 bp (19.39%) number of T's = 206,118,815 bp (30.24%) number of G's = 136,522,967 bp (20.03%) number of N's = 8,332 bp (0%) GC percentage = 39.42% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 6,971,776 number of insertions = 69,104 mapped reads with insertion percentage = 1.15% number of deletions = 148,153 mapped reads with deletion percentage = 2.5% homopolymer indels = 42.82% >>>>>>> Coverage mean coverageData = 0.2203X std coverageData = 3.309X There is a 4.46% of reference with a coverageData >= 1X There is a 3.56% of reference with a coverageData >= 2X There is a 2.76% of reference with a coverageData >= 3X There is a 2.29% of reference with a coverageData >= 4X There is a 1.75% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 1.07% of reference with a coverageData >= 7X There is a 0.88% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.02% 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 0.01% 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 61772775 0.24783398633939613 1.8122450451650645 chr2 243199373 51934762 0.2135480916720949 9.78876253573892 chr3 198022430 42935329 0.21682053391628414 1.3580693610187857 chr4 191154276 45142822 0.23615910114404137 1.8192669727633544 chr5 180915260 35544571 0.19647082838672647 1.2828815996369112 chr6 171115067 25879269 0.15123898470027775 1.1526908784468546 chr7 159138663 61065213 0.3837233004778983 3.689936275403732 chr8 146364022 70391284 0.4809329713554879 2.4879081022496 chr9 141213431 24688833 0.17483346183975942 1.6058310639362348 chr10 135534747 26511971 0.19561014121345577 4.121806581115277 chr11 135006516 28858129 0.21375360134469362 1.3926717115302703 chr12 133851895 25841316 0.1930590224367014 1.2795203251394984 chr13 115169878 18456196 0.1602519367086592 1.1722777041938175 chr14 107349540 24034728 0.22389223093084515 1.3877682565796838 chr15 102531392 17119412 0.1669675176164584 1.180980159258876 chr16 90354753 12520167 0.1385667779978326 1.4361925164527614 chr17 81195210 16237700 0.19998347193141072 1.3945568595990854 chr18 78077248 12775633 0.16362811609343608 1.960531310023569 chr19 59128983 8722190 0.1475112467264996 1.301596251057461 chr20 63025520 26829296 0.42568940327664095 1.9335126415611597 chr21 48129895 8528973 0.17720738846407208 1.306423380139988 chr22 51304566 7085133 0.1380994627261831 1.033661871159434 chrMT 16571 1048060 63.24663568885402 50.82992532432674 chrX 155270560 26924735 0.17340528043435924 1.216063427523221 chrY 59373566 1240878 0.02089950265072507 0.8542707889106274