BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238280.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 = 1,753,036 number of mapped reads = 1,594,510 (90.96%) number of supplementary alignments = 18,834 (1.07%) number of secondary alignments = 0 number of mapped bases = 106,059,080 bp number of sequenced bases = 106,001,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,019 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4774 >>>>>>> ACTG content number of A's = 29,484,084 bp (27.81%) number of C's = 19,090,058 bp (18.01%) number of T's = 34,139,948 bp (32.21%) number of G's = 23,221,274 bp (21.91%) number of N's = 66,137 bp (0.06%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 930,296 number of insertions = 8,687 mapped reads with insertion percentage = 0.54% number of deletions = 34,199 mapped reads with deletion percentage = 2.12% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.0343X std coverageData = 0.3839X There is a 2.83% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 11459713 0.04597666779734924 0.6301834945954276 chr2 243199373 13682304 0.05625961872854006 0.526903313194176 chr3 198022430 3117938 0.015745377935216732 0.15453766628579158 chr4 191154276 11165495 0.05841090889329622 0.29470833933168117 chr5 180915260 1234127 0.006821574918555793 0.11125024405659692 chr6 171115067 5928988 0.03464912882277047 0.26595303011983623 chr7 159138663 5246134 0.03296580416790356 0.3304472667384407 chr8 146364022 7516809 0.05135694480983858 0.4904325907768578 chr9 141213431 3826890 0.02710004262979773 0.44664547071165084 chr10 135534747 10113229 0.07461724187967828 0.4856517526007239 chr11 135006516 2603572 0.01928478770609857 0.26234197895844685 chr12 133851895 1770094 0.013224272992175419 0.1494968655629764 chr13 115169878 2085431 0.018107434306737738 0.15584814874525926 chr14 107349540 1638444 0.01526270163803217 0.18306552603406118 chr15 102531392 3298473 0.03217037178233179 0.20752159899219816 chr16 90354753 4228707 0.04680115721195099 0.3226697953634271 chr17 81195210 866592 0.010672944869531097 0.16470987027864847 chr18 78077248 3130245 0.04009164103734804 0.9880288076525965 chr19 59128983 1108844 0.01875296925029135 0.39136746474564754 chr20 63025520 3592274 0.056997133859427104 0.2802695598835057 chr21 48129895 1858160 0.038607189980364595 0.2536784167468889 chr22 51304566 663501 0.012932591613775662 0.12976789155362928 chrMT 16571 2570 0.15509021785046165 0.4435020998979175 chrX 155270560 5596602 0.03604419279482215 0.24859327488410032 chrY 59373566 323944 0.0054560307191250735 0.16817169277236182