BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472439.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,724,004 number of mapped reads = 17,565,732 (99.11%) number of supplementary alignments = 64,913 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,808,439 number of mapped paired reads (second in pair) = 8,757,293 number of mapped paired reads (both in pair) = 17,480,782 number of mapped paired reads (singletons) = 84,950 number of mapped bases = 1,721,364,343 bp number of sequenced bases = 1,721,163,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,287,809 duplication rate = 47.37% >>>>>>> Insert size mean insert size = 18,596.7228 std insert size = 1,383,962.7258 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 54.7794 >>>>>>> ACTG content number of A's = 458,685,958 bp (26.65%) number of C's = 402,859,965 bp (23.41%) number of T's = 460,204,730 bp (26.74%) number of G's = 399,199,093 bp (23.19%) number of N's = 213,407 bp (0.01%) GC percentage = 46.6% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 8,908,996 number of insertions = 101,715 mapped reads with insertion percentage = 0.57% number of deletions = 79,719 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.5561X std coverageData = 18.4623X There is a 4.66% of reference with a coverageData >= 1X There is a 2.08% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 167606626 0.6724421601340764 21.2121359246519 chr2 243199373 161432971 0.6637885986655072 21.2928627666979 chr3 198022430 128565759 0.6492484664489775 15.342042952212047 chr4 191154276 52201155 0.27308389899685004 12.512821091971544 chr5 180915260 66294128 0.3664374580673847 11.909905516088882 chr6 171115067 127731160 0.7464635478300692 18.843419940906116 chr7 159138663 122609530 0.7704572081267266 22.476745246140172 chr8 146364022 155623161 1.0632610314575806 30.161518332500833 chr9 141213431 74182464 0.5253215892757397 21.168087420462538 chr10 135534747 41626275 0.3071262235063603 12.114191082610665 chr11 135006516 47195990 0.3495830527172481 15.345055700264174 chr12 133851895 59207379 0.44233500765902495 12.264188271269894 chr13 115169878 65085776 0.5651284618014443 19.318392663813974 chr14 107349540 31474063 0.2931923415787343 8.08722245244672 chr15 102531392 29787867 0.29052435960295947 9.038221512646262 chr16 90354753 105597269 1.1686963385313 31.546760286921923 chr17 81195210 43685174 0.5380264919568531 12.043067812091618 chr18 78077248 9136756 0.11702200364439075 5.181049973221945 chr19 59128983 37889469 0.6407935174531921 17.94725461718294 chr20 63025520 72828568 1.1555409300867332 33.960003971158415 chr21 48129895 11235324 0.2334375339900492 11.17896193952378 chr22 51304566 21979037 0.4284031366720849 14.825248361360101 chrMT 16571 5489 0.33124132520668637 0.7394370659475138 chrX 155270560 88045119 0.56704322442065 17.902620881704536 chrY 59373566 337834 0.0056899732113109055 0.3597282006430361