BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003984.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,634,913 number of mapped reads = 3,072,254 (84.52%) number of supplementary alignments = 19,396 (0.53%) number of secondary alignments = 0 number of mapped bases = 201,885,405 bp number of sequenced bases = 201,800,330 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,137 duplication rate = 4.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6366 >>>>>>> ACTG content number of A's = 54,959,527 bp (27.23%) number of C's = 35,435,437 bp (17.56%) number of T's = 66,830,083 bp (33.12%) number of G's = 44,554,179 bp (22.08%) number of N's = 21,104 bp (0.01%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,813,517 number of insertions = 17,310 mapped reads with insertion percentage = 0.56% number of deletions = 52,052 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.0652X std coverageData = 0.6311X There is a 5.27% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17348379 0.0696021495569313 1.2299121938290904 chr2 243199373 14334755 0.058942401138509515 0.7895980652300197 chr3 198022430 15632657 0.07894387014642736 0.33609075952424017 chr4 191154276 12323198 0.06446728923814396 0.33319839962599684 chr5 180915260 8998937 0.04974117164024748 0.27349883030193906 chr6 171115067 11935299 0.06975013486100555 0.3843523643633495 chr7 159138663 14679736 0.09224493736006818 1.06346405124442 chr8 146364022 13979289 0.09551041853714569 0.8782258710398257 chr9 141213431 6030950 0.04270804807511546 0.5018915900902878 chr10 135534747 10635284 0.0784690585654762 0.5570733707082974 chr11 135006516 9682732 0.07172047903228612 0.47935896098826736 chr12 133851895 10452913 0.07809312673533685 0.346906181342796 chr13 115169878 6726211 0.058402519103128686 0.2909303484112711 chr14 107349540 4170374 0.038848550259274514 0.2668881391212498 chr15 102531392 5346553 0.05214552241717346 0.28288965841681385 chr16 90354753 5261965 0.05823672607460949 0.3271518064744505 chr17 81195210 4887939 0.06019984430116013 0.3324367257519121 chr18 78077248 5459398 0.06992303314788964 1.0408530904367064 chr19 59128983 3420447 0.05784721512967676 0.7591783696398687 chr20 63025520 4527392 0.0718342665003002 0.354746969446761 chr21 48129895 2925972 0.060793234641380374 0.31284845047642523 chr22 51304566 1469539 0.028643434972240093 0.1931739501774507 chrMT 16571 136028 8.208798503409572 5.5166952223663674 chrX 155270560 11027313 0.07101998601666665 0.3819153045532115 chrY 59373566 492145 0.008288958086162451 0.1756433693546573