BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779277.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 = 11,489,966 number of mapped reads = 10,773,093 (93.76%) number of supplementary alignments = 25,458 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,442,939 number of mapped paired reads (second in pair) = 5,330,154 number of mapped paired reads (both in pair) = 10,638,964 number of mapped paired reads (singletons) = 134,129 number of mapped bases = 857,033,633 bp number of sequenced bases = 856,865,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,545 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 37,267.4254 std insert size = 1,825,413.895 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.5611 >>>>>>> ACTG content number of A's = 263,021,703 bp (30.7%) number of C's = 164,209,528 bp (19.16%) number of T's = 262,400,305 bp (30.62%) number of G's = 167,072,628 bp (19.5%) number of N's = 161,772 bp (0.02%) GC percentage = 38.66% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,281,233 number of insertions = 63,643 mapped reads with insertion percentage = 0.58% number of deletions = 80,203 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.2768X std coverageData = 1.4025X There is a 12.72% of reference with a coverageData >= 1X There is a 5.51% of reference with a coverageData >= 2X There is a 2.89% of reference with a coverageData >= 3X There is a 1.72% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.74% of reference with a coverageData >= 6X There is a 0.52% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% 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 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 82696049 0.3317787079856463 1.5138502302986756 chr2 243199373 48593022 0.1998073490099006 0.8439429633826884 chr3 198022430 38204720 0.19293127551257702 0.8163818563923161 chr4 191154276 48266408 0.2524997557470281 0.9959826429031088 chr5 180915260 88093070 0.48693001353230236 1.5081855634560353 chr6 171115067 24080415 0.14072644462103387 0.7072952128675631 chr7 159138663 88393241 0.5554479303373311 3.895770276885082 chr8 146364022 53811068 0.36765229094346696 1.1915581651504485 chr9 141213431 32826863 0.23246275348978668 1.039214340488123 chr10 135534747 14656109 0.10813543629516643 1.4458281394080157 chr11 135006516 60412033 0.4474749426168438 1.4568431938811153 chr12 133851895 55106738 0.4116993487466128 1.34639901090251 chr13 115169878 44470485 0.38612947909869283 1.2591080321364714 chr14 107349540 32263156 0.3005430298071142 1.1043687251112497 chr15 102531392 31950068 0.3116125449657408 1.1460172432300217 chr16 90354753 9043811 0.10009225524638421 0.5247076189821274 chr17 81195210 16812160 0.20705851983140386 0.8549614726958836 chr18 78077248 17317307 0.221797097664098 0.9096226426369948 chr19 59128983 5777647 0.09771260567765896 0.8085483107083193 chr20 63025520 19517542 0.3096768102825649 1.0333754269695439 chr21 48129895 8150776 0.16934954875758612 0.7815092952770368 chr22 51304566 3339547 0.06509258844524676 0.41484673022251817 chrMT 16571 1066 0.06432924989439381 0.2608371675535228 chrX 155270560 32865851 0.2116682711777429 0.9558272681427065 chrY 59373566 384481 0.00647562587027365 0.13239892467369904