BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234136.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 = 2,546,437 number of mapped reads = 1,557,624 (61.17%) number of supplementary alignments = 6,440 (0.25%) number of secondary alignments = 0 number of mapped bases = 93,864,130 bp number of sequenced bases = 93,797,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,486 duplication rate = 5.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4949 >>>>>>> ACTG content number of A's = 24,505,684 bp (26.13%) number of C's = 17,004,328 bp (18.13%) number of T's = 29,474,111 bp (31.42%) number of G's = 22,792,491 bp (24.3%) number of N's = 20,908 bp (0.02%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 898,555 number of insertions = 8,171 mapped reads with insertion percentage = 0.52% number of deletions = 37,527 mapped reads with deletion percentage = 2.37% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2909X There is a 2.37% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 8246253 0.03308418236598897 0.40277162200333005 chr2 243199373 6651498 0.027349980051141004 0.32930709709067757 chr3 198022430 7559383 0.03817437751874876 0.24791229384131785 chr4 191154276 4638991 0.02426830880832611 0.21166332722890524 chr5 180915260 5445134 0.030097704306425006 0.22428459736186687 chr6 171115067 5989353 0.03500190313457318 0.2985424469214303 chr7 159138663 5729872 0.03600553059818028 0.4519856020577433 chr8 146364022 4543485 0.031042362309502535 0.31234307709160586 chr9 141213431 3764730 0.026659857871451337 0.26469998382266097 chr10 135534747 4641027 0.03424234082201814 0.2682211893309167 chr11 135006516 4373122 0.03239193284567095 0.30771503595195937 chr12 133851895 3775531 0.028206780337327313 0.21303858101126508 chr13 115169878 3370228 0.02926310297906194 0.2457507813000573 chr14 107349540 3835741 0.03573132218358831 0.25829812834486066 chr15 102531392 2268694 0.022126823363521682 0.19846782520999134 chr16 90354753 2665871 0.02950449103657004 0.2384154300085762 chr17 81195210 2650029 0.03263775042887382 0.2509046979615601 chr18 78077248 2129859 0.02727886874291471 0.3955605768568068 chr19 59128983 2599648 0.04396571474939794 0.3583179934145807 chr20 63025520 2240456 0.0355483937300319 0.2518745247695709 chr21 48129895 1394888 0.028981737857520777 0.22009470086332036 chr22 51304566 992620 0.019347595689631212 0.1735032072729086 chrMT 16571 68045 4.106269989741114 4.661561185402165 chrX 155270560 3924122 0.025272801231605014 0.2165340166868027 chrY 59373566 365550 0.006156780274912239 0.10839937773059487