BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 935,654 number of mapped reads = 857,023 (91.6%) number of supplementary alignments = 2,916 (0.31%) number of secondary alignments = 0 number of mapped bases = 50,011,651 bp number of sequenced bases = 49,995,945 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,201 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9743 >>>>>>> ACTG content number of A's = 12,330,533 bp (24.66%) number of C's = 9,389,805 bp (18.78%) number of T's = 16,045,728 bp (32.09%) number of G's = 12,229,215 bp (24.46%) number of N's = 664 bp (0%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 254,978 number of insertions = 3,192 mapped reads with insertion percentage = 0.37% number of deletions = 9,323 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.13% >>>>>>> Coverage mean coverageData = 0.0162X std coverageData = 0.1766X There is a 1.49% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4854572 0.01947666962883916 0.306178129292855 chr2 243199373 3878060 0.015946011505547756 0.1886831187364303 chr3 198022430 2730156 0.013787104824438323 0.12456107872125015 chr4 191154276 2761794 0.014447984412339278 0.14005918545650178 chr5 180915260 2731442 0.015097908269319017 0.13058472067106672 chr6 171115067 2144189 0.01253068498053418 0.14039278367348645 chr7 159138663 2472976 0.015539756042816572 0.204984567535962 chr8 146364022 5042191 0.03444966140654429 0.2193867236679803 chr9 141213431 2087161 0.014780187587114146 0.15130649583028838 chr10 135534747 2593153 0.019132754200662655 0.18249801875025018 chr11 135006516 1714075 0.012696239046713863 0.15807719032497947 chr12 133851895 2278423 0.017021970439790934 0.1391498008324324 chr13 115169878 1098538 0.009538414202366351 0.10283900691236944 chr14 107349540 1198377 0.011163317513982826 0.11371377616734746 chr15 102531392 1327675 0.012948961036245368 0.12035476913011349 chr16 90354753 1543841 0.017086439271213547 0.1438112522379019 chr17 81195210 1734796 0.021365743126965247 0.1602717802488239 chr18 78077248 1165250 0.014924322127747126 0.2594394478236993 chr19 59128983 1020513 0.017259099484257998 0.22767619281081355 chr20 63025520 1423624 0.022588056393664027 0.15990300537041394 chr21 48129895 674429 0.014012683800785354 0.13537418116350206 chr22 51304566 415238 0.008093587615574022 0.09497052686583567 chrMT 16571 2632 0.1588316939231187 0.42788809905036435 chrX 155270560 2943418 0.018956703704810493 0.15567467907721286 chrY 59373566 175128 0.002949595447913639 0.09924712549064689