BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779386.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 = 13,770,384 number of mapped reads = 13,178,274 (95.7%) number of supplementary alignments = 51,156 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,634,595 number of mapped paired reads (second in pair) = 6,543,679 number of mapped paired reads (both in pair) = 13,061,226 number of mapped paired reads (singletons) = 117,048 number of mapped bases = 1,047,629,139 bp number of sequenced bases = 1,047,402,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 585,478 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 33,417.6832 std insert size = 1,687,635.0077 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.7115 >>>>>>> ACTG content number of A's = 313,409,218 bp (29.92%) number of C's = 209,051,600 bp (19.96%) number of T's = 312,371,015 bp (29.82%) number of G's = 212,333,427 bp (20.27%) number of N's = 237,011 bp (0.02%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 3,337,555 number of insertions = 93,575 mapped reads with insertion percentage = 0.7% number of deletions = 108,552 mapped reads with deletion percentage = 0.81% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.3384X std coverageData = 1.6148X There is a 13.38% of reference with a coverageData >= 1X There is a 6.58% of reference with a coverageData >= 2X There is a 3.83% of reference with a coverageData >= 3X There is a 2.51% of reference with a coverageData >= 4X There is a 1.75% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 0.94% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.55% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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% 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 38413073 0.1541142519360062 2.820957408721265 chr2 243199373 84675744 0.3481741871102604 1.1855647125981894 chr3 198022430 73632640 0.37183989712680526 1.167470906264906 chr4 191154276 101391158 0.5304153279835603 1.851926981956858 chr5 180915260 105157510 0.5812528473275278 1.6686964666406052 chr6 171115067 30515518 0.17833331999922603 1.1442673471702651 chr7 159138663 82501305 0.5184240174243515 1.618486602833109 chr8 146364022 28195658 0.1926406340487145 0.8539960877533301 chr9 141213431 53572363 0.3793715839961427 1.6050179656465458 chr10 135534747 38722078 0.2856985301341213 2.0523302295932586 chr11 135006516 61266660 0.4538052074464317 1.6012212955280176 chr12 133851895 57502735 0.4295997079458606 1.5699246817524735 chr13 115169878 38707731 0.3360924893920614 1.1376167759311138 chr14 107349540 32783825 0.3053932508700084 1.291660652675154 chr15 102531392 13836656 0.13495043547248436 0.8112652333939168 chr16 90354753 42123724 0.46620374248602064 2.2232825770997247 chr17 81195210 22120482 0.2724358000921483 1.0890154566965788 chr18 78077248 36337715 0.4654072208077826 1.6406314905375765 chr19 59128983 9469415 0.1601484503800784 1.5680352103174733 chr20 63025520 20721247 0.3287755023679297 1.512839344223159 chr21 48129895 13663607 0.28389023080145925 1.24420402788849 chr22 51304566 22542065 0.4393773645799869 2.059654114392174 chrMT 16571 160 0.00965542212298594 0.09778647629714904 chrX 155270560 35879191 0.2310752984983116 0.997261201203136 chrY 59373566 3896879 0.06563323146196069 0.5091772709533565