BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779093.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 = 25,792,926 number of mapped reads = 24,897,478 (96.53%) number of supplementary alignments = 130,053 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,590,688 number of mapped paired reads (second in pair) = 12,306,790 number of mapped paired reads (both in pair) = 24,528,112 number of mapped paired reads (singletons) = 369,366 number of mapped bases = 2,488,401,433 bp number of sequenced bases = 2,487,803,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 682,362 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 71,763.4534 std insert size = 2,567,813.5828 median insert size = 285 >>>>>>> Mapping quality mean mapping quality = 53.321 >>>>>>> ACTG content number of A's = 766,823,014 bp (30.82%) number of C's = 474,167,676 bp (19.06%) number of T's = 764,275,760 bp (30.72%) number of G's = 481,693,192 bp (19.36%) number of N's = 843,926 bp (0.03%) GC percentage = 38.42% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 11,990,073 number of insertions = 216,892 mapped reads with insertion percentage = 0.86% number of deletions = 266,542 mapped reads with deletion percentage = 1.05% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.8038X std coverageData = 1.9794X There is a 32.19% of reference with a coverageData >= 1X There is a 17.07% of reference with a coverageData >= 2X There is a 9.98% of reference with a coverageData >= 3X There is a 6.23% of reference with a coverageData >= 4X There is a 4.07% of reference with a coverageData >= 5X There is a 2.75% of reference with a coverageData >= 6X There is a 1.92% of reference with a coverageData >= 7X There is a 1.37% of reference with a coverageData >= 8X There is a 1% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.56% of reference with a coverageData >= 11X There is a 0.43% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 194937444 0.782094115625092 2.116154608091376 chr2 243199373 190742034 0.784303148676292 1.8944868778211348 chr3 198022430 205549134 1.0380093507589014 2.023342193384384 chr4 191154276 205268864 1.0738387249051127 2.0311467695531347 chr5 180915260 111638758 0.6170776196546384 1.47162123190713 chr6 171115067 151162268 0.8833954288782764 1.8752811774270817 chr7 159138663 216266287 1.358980168131738 3.4759138853630236 chr8 146364022 230017801 1.571546052485494 2.5387618268191505 chr9 141213431 91275841 0.6463679860593431 1.7527015128252508 chr10 135534747 34845472 0.25709622640163265 1.325603052121269 chr11 135006516 114044809 0.8447355903918 1.8767592252275558 chr12 133851895 100592371 0.7515199616710694 1.8061750868388853 chr13 115169878 68129383 0.591555571501083 1.4832984424124034 chr14 107349540 100881915 0.9397517213394673 2.035359378885318 chr15 102531392 55145862 0.5378436879116983 1.5618300183233058 chr16 90354753 34420686 0.3809504741825812 1.1444540594347332 chr17 81195210 31128564 0.3833793151098445 1.306224381105232 chr18 78077248 92191703 1.1807755186248368 2.0960421364983883 chr19 59128983 16968119 0.28696788172392546 1.1777521746558957 chr20 63025520 36372953 0.5771146830680651 1.516145632963695 chr21 48129895 12704080 0.26395403522072924 0.9150010682264019 chr22 51304566 9160905 0.17855925338107334 0.6792537106664616 chrMT 16571 4975 0.30022328163659406 0.6341225987700101 chrX 155270560 183306030 1.1805588258327915 2.3646934226119596 chrY 59373566 1645175 0.02770887973951236 0.41863251860635037