BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716993.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 = 1,794,472 number of mapped reads = 1,612,882 (89.88%) number of supplementary alignments = 8,353 (0.47%) number of secondary alignments = 0 number of mapped bases = 93,376,985 bp number of sequenced bases = 93,350,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,249 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8709 >>>>>>> ACTG content number of A's = 24,014,439 bp (25.73%) number of C's = 17,739,440 bp (19%) number of T's = 29,659,780 bp (31.77%) number of G's = 21,935,401 bp (23.5%) number of N's = 1,180 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 473,024 number of insertions = 6,560 mapped reads with insertion percentage = 0.4% number of deletions = 17,046 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.65% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.3123X There is a 2.68% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7418802 0.02976442734720408 0.39300777052939845 chr2 243199373 8861738 0.03643816137634533 0.36862965565397815 chr3 198022430 7659463 0.03867977481136859 0.24352210255894133 chr4 191154276 5087523 0.026614748602327893 0.19031930593843863 chr5 180915260 4581282 0.025322805826329963 0.17615487986447528 chr6 171115067 5015975 0.02931346191741257 0.2057058854339838 chr7 159138663 6073171 0.038162762496000105 0.7259965909794217 chr8 146364022 7649400 0.052262843665228056 0.32549316855222094 chr9 141213431 3748014 0.026541483862112237 0.20438233093140074 chr10 135534747 4336892 0.031998377508315266 0.48409011288715637 chr11 135006516 2748951 0.020361617212609203 0.19743352835119915 chr12 133851895 4274568 0.03193505777411668 0.24126840982215433 chr13 115169878 2377691 0.020645077005291262 0.1566124858767149 chr14 107349540 2904700 0.027058336719468012 0.1825588087705284 chr15 102531392 2155042 0.021018362844425247 0.16398485799167337 chr16 90354753 2692315 0.029797159646930804 0.20191704558600948 chr17 81195210 4086308 0.050326958942528754 0.2581319687267771 chr18 78077248 2213692 0.02835258742726178 0.32445973312945614 chr19 59128983 1800331 0.03044752181853018 0.4113223194453441 chr20 63025520 1989067 0.03155970787706313 0.2143362446514059 chr21 48129895 916710 0.019046582171018657 0.15766714263416784 chr22 51304566 1312085 0.02557442937924862 0.1743024208548604 chrMT 16571 51981 3.1368656085933257 2.552055164096683 chrX 155270560 3216098 0.02071286404840686 0.19032739238029373 chrY 59373566 205186 0.0034558476747042614 0.09213543698509029