BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231828.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 = 5,612,731 number of mapped reads = 4,770,447 (84.99%) number of supplementary alignments = 26,009 (0.46%) number of secondary alignments = 0 number of mapped bases = 302,987,019 bp number of sequenced bases = 302,865,174 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 460,046 duplication rate = 7.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5196 >>>>>>> ACTG content number of A's = 77,400,127 bp (25.56%) number of C's = 54,100,634 bp (17.86%) number of T's = 99,110,010 bp (32.72%) number of G's = 72,140,305 bp (23.82%) number of N's = 114,098 bp (0.04%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,916,020 number of insertions = 19,671 mapped reads with insertion percentage = 0.41% number of deletions = 68,412 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.08% >>>>>>> Coverage mean coverageData = 0.0979X std coverageData = 0.9359X There is a 7.51% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 22623329 0.09076538669887607 1.6356980270991412 chr2 243199373 21232816 0.0873062119284329 1.2770558592526278 chr3 198022430 38339586 0.1936123397738327 0.5473257081763115 chr4 191154276 17449512 0.09128496816885226 0.41868774076570914 chr5 180915260 6611029 0.03654213027690423 0.26770946684119096 chr6 171115067 24516937 0.1432774882412897 0.7494256097537991 chr7 159138663 18603395 0.11690053598100167 1.5024670892307348 chr8 146364022 23801452 0.16261818768549555 1.0408252887765055 chr9 141213431 13932433 0.09866223702191614 0.9011910286618136 chr10 135534747 8248465 0.06085867412288009 0.5804100981442594 chr11 135006516 5364176 0.039732719271120216 0.802261272241828 chr12 133851895 3320216 0.024805147510238837 0.2805994850850977 chr13 115169878 14257670 0.12379686639938961 0.4507179825675023 chr14 107349540 16897315 0.15740463349912817 0.5768284291796963 chr15 102531392 4862715 0.047426596919702406 0.3355320961590655 chr16 90354753 9376070 0.1037695272101513 0.566427001773923 chr17 81195210 3889715 0.04790572005417561 0.2993059449827049 chr18 78077248 9448312 0.12101235945201347 2.2081173772151423 chr19 59128983 7214438 0.12201187360181723 1.0326714651723796 chr20 63025520 7606340 0.1206866678767585 0.4827546523054906 chr21 48129895 4552810 0.09459422257206254 0.442439007897009 chr22 51304566 5528149 0.10775159856142238 0.4085804566228949 chrMT 16571 494325 29.830728380906404 16.16799661773085 chrX 155270560 14023314 0.09031534374578155 0.6098467156091383 chrY 59373566 792500 0.013347690788860484 0.2657533042626494