BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779348.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 = 318,062,820 number of mapped reads = 302,201,094 (95.01%) number of supplementary alignments = 1,437,907 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 152,205,722 number of mapped paired reads (second in pair) = 149,995,372 number of mapped paired reads (both in pair) = 297,426,882 number of mapped paired reads (singletons) = 4,774,212 number of mapped bases = 30,257,651,796 bp number of sequenced bases = 30,250,359,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,547,344 duplication rate = 16.88% >>>>>>> Insert size mean insert size = 63,773.9863 std insert size = 2,448,604.7831 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.6284 >>>>>>> ACTG content number of A's = 9,156,522,219 bp (30.27%) number of C's = 5,957,664,330 bp (19.69%) number of T's = 9,083,696,927 bp (30.03%) number of G's = 6,043,603,051 bp (19.98%) number of N's = 8,872,988 bp (0.03%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 102,731,174 number of insertions = 2,538,928 mapped reads with insertion percentage = 0.83% number of deletions = 3,242,054 mapped reads with deletion percentage = 1.05% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 9.7741X std coverageData = 27.021X There is a 67.83% of reference with a coverageData >= 1X There is a 58.52% of reference with a coverageData >= 2X There is a 51.77% of reference with a coverageData >= 3X There is a 46.58% of reference with a coverageData >= 4X There is a 42.32% of reference with a coverageData >= 5X There is a 38.71% of reference with a coverageData >= 6X There is a 35.59% of reference with a coverageData >= 7X There is a 32.85% of reference with a coverageData >= 8X There is a 30.41% of reference with a coverageData >= 9X There is a 28.24% of reference with a coverageData >= 10X There is a 26.28% of reference with a coverageData >= 11X There is a 24.5% of reference with a coverageData >= 12X There is a 22.89% of reference with a coverageData >= 13X There is a 21.42% of reference with a coverageData >= 14X There is a 20.08% of reference with a coverageData >= 15X There is a 18.84% of reference with a coverageData >= 16X There is a 17.71% of reference with a coverageData >= 17X There is a 16.66% of reference with a coverageData >= 18X There is a 15.7% of reference with a coverageData >= 19X There is a 14.8% of reference with a coverageData >= 20X There is a 13.97% of reference with a coverageData >= 21X There is a 13.2% of reference with a coverageData >= 22X There is a 12.48% of reference with a coverageData >= 23X There is a 11.82% of reference with a coverageData >= 24X There is a 11.19% of reference with a coverageData >= 25X There is a 10.61% of reference with a coverageData >= 26X There is a 10.07% of reference with a coverageData >= 27X There is a 9.56% of reference with a coverageData >= 28X There is a 9.08% of reference with a coverageData >= 29X There is a 8.64% of reference with a coverageData >= 30X There is a 8.21% of reference with a coverageData >= 31X There is a 7.82% of reference with a coverageData >= 32X There is a 7.45% of reference with a coverageData >= 33X There is a 7.1% of reference with a coverageData >= 34X There is a 6.77% of reference with a coverageData >= 35X There is a 6.46% of reference with a coverageData >= 36X There is a 6.16% of reference with a coverageData >= 37X There is a 5.89% of reference with a coverageData >= 38X There is a 5.62% of reference with a coverageData >= 39X There is a 5.38% of reference with a coverageData >= 40X There is a 5.14% of reference with a coverageData >= 41X There is a 4.92% of reference with a coverageData >= 42X There is a 4.71% of reference with a coverageData >= 43X There is a 4.51% of reference with a coverageData >= 44X There is a 4.32% of reference with a coverageData >= 45X There is a 4.14% of reference with a coverageData >= 46X There is a 3.97% of reference with a coverageData >= 47X There is a 3.81% of reference with a coverageData >= 48X There is a 3.65% of reference with a coverageData >= 49X There is a 3.51% of reference with a coverageData >= 50X There is a 3.37% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2092958440 8.397003913583028 21.87926732393838 chr2 243199373 2544909929 10.464294778424449 20.729986550169205 chr3 198022430 2845623745 14.370209198018628 22.355523952621105 chr4 191154276 1759144355 9.202746555353018 16.791245319023208 chr5 180915260 1313811396 7.262026409491383 14.07922329938328 chr6 171115067 2334188480 13.641045881716542 22.24706460110405 chr7 159138663 2791902705 17.54383662881471 79.65217150700778 chr8 146364022 2242191497 15.319280423982883 22.883741162288942 chr9 141213431 1133639997 8.027848264659754 20.324829109423035 chr10 135534747 428995450 3.165206410131861 35.872175959416474 chr11 135006516 1596938486 11.828603043130155 20.868460401181796 chr12 133851895 1532673432 11.450517245198508 22.237277816805662 chr13 115169878 970250297 8.424514411658924 14.903867745311391 chr14 107349540 1310985800 12.212309433277497 20.762116005872613 chr15 102531392 736143062 7.179684656968278 15.040692209995912 chr16 90354753 790632602 8.750315570006594 16.894443577795045 chr17 81195210 496990927 6.120938993815029 14.35841642273715 chr18 78077248 797632604 10.215941576219489 20.128715346017607 chr19 59128983 385890444 6.5262486249763505 19.882312255258384 chr20 63025520 904135827 14.345551246542671 24.87750192496027 chr21 48129895 301526861 6.264855990232266 14.13915805522312 chr22 51304566 244257507 4.76093116156562 10.618473336668648 chrMT 16571 58896 3.5541608834711242 5.598772357017942 chrX 155270560 686148446 4.41905050126695 12.592180405670657 chrY 59373566 16020611 0.26982733359825484 4.302801492279174