BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068938.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 = 2,838,634 number of mapped reads = 2,244,234 (79.06%) number of supplementary alignments = 8,499 (0.3%) number of secondary alignments = 0 number of mapped bases = 142,606,918 bp number of sequenced bases = 142,527,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,462 duplication rate = 7.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4311 >>>>>>> ACTG content number of A's = 38,022,169 bp (26.68%) number of C's = 23,846,593 bp (16.73%) number of T's = 48,172,496 bp (33.8%) number of G's = 32,149,323 bp (22.56%) number of N's = 336,741 bp (0.24%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 1,584,988 number of insertions = 12,134 mapped reads with insertion percentage = 0.54% number of deletions = 50,785 mapped reads with deletion percentage = 2.24% homopolymer indels = 49.1% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.4465X There is a 3.21% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12989828 0.05211552913242291 0.7182909521444356 chr2 243199373 13904023 0.057171294598691254 0.45595613828114706 chr3 198022430 11870640 0.059945936427504704 0.3399650486498844 chr4 191154276 6989664 0.03656556445538262 0.27196345191658805 chr5 180915260 7625511 0.04214962850563297 0.2801481640151155 chr6 171115067 7302048 0.04267331993622747 0.31174641718645124 chr7 159138663 7876505 0.049494603332189614 0.6665307474967886 chr8 146364022 8830964 0.06033561991074555 0.5912776480869467 chr9 141213431 7533543 0.05334862942321683 0.5170178478425567 chr10 135534747 6171278 0.04553281085919613 0.42455529292618016 chr11 135006516 8418753 0.0623581235145717 0.5197510236571643 chr12 133851895 7964930 0.05950554528944099 0.347322664191856 chr13 115169878 3077838 0.02672433151314096 0.22121261409792572 chr14 107349540 3228844 0.03007785594609907 0.29740865181104814 chr15 102531392 3551993 0.03464298036644231 0.2526580424571018 chr16 90354753 3695364 0.040898390812932665 0.3107382093061396 chr17 81195210 1971786 0.024284511364648233 0.2663326091687673 chr18 78077248 1908248 0.024440513067263848 0.7083403028988419 chr19 59128983 1858988 0.03143953955710688 0.5455403012870097 chr20 63025520 2769281 0.043939042470415156 0.30458135748351833 chr21 48129895 1935455 0.040213156500756964 0.31241140798174055 chr22 51304566 1260288 0.024564831130235075 0.2057102435530023 chrMT 16571 123509 7.45332206867419 7.730392008888335 chrX 155270560 9361066 0.060288737285419725 0.3945722046390643 chrY 59373566 386571 0.006510826720429762 0.1469614247942907