BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779207.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 8,482,370 number of mapped reads = 8,219,882 (96.91%) number of supplementary alignments = 20,726 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,156,436 number of mapped paired reads (second in pair) = 4,063,446 number of mapped paired reads (both in pair) = 8,114,474 number of mapped paired reads (singletons) = 105,408 number of mapped bases = 653,640,666 bp number of sequenced bases = 653,506,382 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,677 duplication rate = 0.8% >>>>>>> Insert size mean insert size = 53,772.5317 std insert size = 2,189,405.5566 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.0246 >>>>>>> ACTG content number of A's = 199,164,438 bp (30.48%) number of C's = 126,454,374 bp (19.35%) number of T's = 199,048,835 bp (30.46%) number of G's = 128,718,342 bp (19.7%) number of N's = 120,393 bp (0.02%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,887,095 number of insertions = 51,549 mapped reads with insertion percentage = 0.62% number of deletions = 64,988 mapped reads with deletion percentage = 0.78% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.2111X std coverageData = 0.6488X There is a 15.19% of reference with a coverageData >= 1X There is a 3.96% of reference with a coverageData >= 2X There is a 1.19% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 46397651 0.18614858736901602 0.8326634319107951 chr2 243199373 52040320 0.21398213062004892 0.5783460029696955 chr3 198022430 47874114 0.24176106716799708 0.6206033682353747 chr4 191154276 43255126 0.22628385252548575 0.6055874223329306 chr5 180915260 38948715 0.21528706312557602 0.5838298565634001 chr6 171115067 36992929 0.21618744420676878 0.5944455091022866 chr7 159138663 56255361 0.3534990173946604 1.0243568161662144 chr8 146364022 42577772 0.290903265831271 0.679890697972447 chr9 141213431 24619750 0.17434425199965575 0.5526760407347204 chr10 135534747 20955534 0.15461373901409947 0.7941240278355334 chr11 135006516 31867034 0.2360407108053955 0.6136686287563867 chr12 133851895 27748044 0.20730408037928788 0.5738413861205195 chr13 115169878 25171947 0.21856363345283739 0.5875475095847031 chr14 107349540 22598099 0.2105095094026486 0.5783606438044928 chr15 102531392 17358368 0.16929808189866377 0.5209736299710117 chr16 90354753 11981756 0.13260792157773924 0.45898485611868034 chr17 81195210 12544031 0.15449225391497848 0.4920943727585073 chr18 78077248 18425141 0.23598604551225985 0.6165343579735747 chr19 59128983 8656996 0.14640867406767338 0.6638024572986166 chr20 63025520 15231105 0.24166567764930777 0.6548890843328563 chr21 48129895 9465937 0.1966747901693947 0.5745587043895317 chr22 51304566 5594335 0.10904165917707988 0.4076535347948297 chrMT 16571 931 0.05618248747812443 0.27821925964863453 chrX 155270560 36629936 0.23591037476776022 0.6340954855100853 chrY 59373566 449734 0.007574650308185969 0.11776333451994005