BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548921.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,386,655 number of mapped reads = 5,582,903 (87.42%) number of secondary alignments = 0 number of mapped bases = 221,027,874 bp number of sequenced bases = 221,004,029 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,356 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1966 >>>>>>> ACTG content number of A's = 65,120,694 bp (29.47%) number of C's = 45,351,172 bp (20.52%) number of T's = 65,362,941 bp (29.58%) number of G's = 45,167,251 bp (20.44%) number of N's = 1,971 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 629,798 number of insertions = 7,232 mapped reads with insertion percentage = 0.13% number of deletions = 18,083 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.44% >>>>>>> Coverage mean coverageData = 0.0714X std coverageData = 0.7731X There is a 6.15% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 17358874 0.06964425577098161 0.8356209269987103 chr2 243199373 18717398 0.07696318361807619 0.4500272964989752 chr3 198022430 15218488 0.07685234445411057 0.312129163647039 chr4 191154276 14935939 0.07813552127915778 0.32281687449726876 chr5 180915260 13846346 0.07653498107345948 0.3167782816113807 chr6 171115067 12998316 0.07596242825303046 0.3371017174493526 chr7 159138663 12338490 0.07753294999091452 0.6833125815234322 chr8 146364022 11465114 0.07833287062854832 2.8769809591823767 chr9 141213431 9380782 0.06642981431419226 0.44056863902634164 chr10 135534747 10168314 0.07502366902267504 0.41420975927232945 chr11 135006516 9984016 0.07395210465248951 0.46340129782796025 chr12 133851895 10055300 0.07512258231383276 0.31835854041035283 chr13 115169878 7297361 0.06336171511790609 0.27937560680519574 chr14 107349540 6717599 0.06257687736715034 0.32910980247703453 chr15 102531392 6214599 0.06061167100901156 0.275034360240183 chr16 90354753 5964789 0.06601522113618084 0.31724736977962104 chr17 81195210 5469221 0.06735891193581493 0.31077259338819513 chr18 78077248 5862983 0.07509208060202122 0.7808815456372437 chr19 59128983 4079026 0.06898522168054201 0.799737277610119 chr20 63025520 4331309 0.0687230981989518 0.3042110158869039 chr21 48129895 2819693 0.05858506443864048 0.3097581267217609 chr22 51304566 2288147 0.0445992857633763 0.27281926969374204 chrMT 16571 6342 0.3827167943998552 0.6983177666445274 chrX 155270560 12827793 0.08261574505817458 0.39624413971795963 chrY 59373566 681635 0.011480445691943111 0.1569920138505213