BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779100.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 = 22,088,712 number of mapped reads = 21,497,071 (97.32%) number of supplementary alignments = 117,348 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,826,506 number of mapped paired reads (second in pair) = 10,670,565 number of mapped paired reads (both in pair) = 21,265,304 number of mapped paired reads (singletons) = 231,767 number of mapped bases = 2,147,574,137 bp number of sequenced bases = 2,147,078,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 558,800 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 64,570.0207 std insert size = 2,437,081.293 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.6652 >>>>>>> ACTG content number of A's = 655,617,835 bp (30.54%) number of C's = 415,624,708 bp (19.36%) number of T's = 653,626,619 bp (30.44%) number of G's = 421,344,129 bp (19.62%) number of N's = 865,015 bp (0.04%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 8,948,088 number of insertions = 179,954 mapped reads with insertion percentage = 0.83% number of deletions = 221,672 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.6937X std coverageData = 1.8444X There is a 32.51% of reference with a coverageData >= 1X There is a 16.24% of reference with a coverageData >= 2X There is a 8.33% of reference with a coverageData >= 3X There is a 4.54% of reference with a coverageData >= 4X There is a 2.58% of reference with a coverageData >= 5X There is a 1.52% of reference with a coverageData >= 6X There is a 0.93% of reference with a coverageData >= 7X There is a 0.59% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% 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 0.02% 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 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 142033436 0.5698418540750596 2.4097568763183848 chr2 243199373 181346109 0.7456684890384154 1.657308650134487 chr3 198022430 167313224 0.8449205678366839 1.5382230191445545 chr4 191154276 178537472 0.9339967472137531 1.6376623022870866 chr5 180915260 121367792 0.6708543657400708 1.3275265776077845 chr6 171115067 153618751 0.8977511664709221 1.6452375547734424 chr7 159138663 212042040 1.3324357261943316 3.9164424058562264 chr8 146364022 136742690 0.934264364503457 1.6435112264501683 chr9 141213431 86695329 0.6139311847751933 1.440260204154735 chr10 135534747 47330608 0.34921382927729966 2.884991775428743 chr11 135006516 81840736 0.6061984148972483 1.2892139594170748 chr12 133851895 86589796 0.6469075092287636 1.3396964251251116 chr13 115169878 70014639 0.6079249211325899 1.3058677867303354 chr14 107349540 71730041 0.6681914147000537 1.4016349697651271 chr15 102531392 39669909 0.38690500759026075 1.1118507904998318 chr16 90354753 41844665 0.4631152607987319 1.0816090984969822 chr17 81195210 40523842 0.4990915350794708 1.390702080692942 chr18 78077248 45221482 0.5791889847347078 1.29040054372941 chr19 59128983 28247727 0.4777306418410748 1.6311467049342436 chr20 63025520 42912952 0.6808821569421403 1.4061016697051887 chr21 48129895 24813997 0.5155630819473012 1.221781761946926 chr22 51304566 12901278 0.2514645187720719 0.8001912605440746 chrMT 16571 3020 0.1822460925713596 0.5046988963324409 chrX 155270560 133005858 0.8566070606044056 1.6584664941091594 chrY 59373566 1226744 0.020661450585602353 0.3316600333169677