BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779383.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 = 13,114,892 number of mapped reads = 12,414,721 (94.66%) number of supplementary alignments = 90,035 (0.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,245,786 number of mapped paired reads (second in pair) = 6,168,935 number of mapped paired reads (both in pair) = 12,292,272 number of mapped paired reads (singletons) = 122,449 number of mapped bases = 985,619,789 bp number of sequenced bases = 985,406,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,252,944 duplication rate = 8.57% >>>>>>> Insert size mean insert size = 89,056.2611 std insert size = 2,821,243.3856 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.7408 >>>>>>> ACTG content number of A's = 305,001,474 bp (30.95%) number of C's = 187,143,453 bp (18.99%) number of T's = 301,575,195 bp (30.6%) number of G's = 191,467,167 bp (19.43%) number of N's = 219,452 bp (0.02%) GC percentage = 38.42% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,762,003 number of insertions = 95,638 mapped reads with insertion percentage = 0.76% number of deletions = 106,983 mapped reads with deletion percentage = 0.85% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.3184X std coverageData = 9.0245X There is a 8.6% of reference with a coverageData >= 1X There is a 4.31% of reference with a coverageData >= 2X There is a 2.72% of reference with a coverageData >= 3X There is a 1.92% of reference with a coverageData >= 4X There is a 1.44% of reference with a coverageData >= 5X There is a 1.13% of reference with a coverageData >= 6X There is a 0.91% of reference with a coverageData >= 7X There is a 0.75% of reference with a coverageData >= 8X There is a 0.63% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.13% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 76721214 0.3078075139479793 9.51946859034237 chr2 243199373 79776391 0.3280287692189075 7.581108298975147 chr3 198022430 78819315 0.3980322582648844 15.517286222685625 chr4 191154276 83561383 0.43714106086750576 3.5803891145816715 chr5 180915260 97748275 0.5402986735336753 8.499913458393408 chr6 171115067 38171055 0.22307243698183515 5.264059310807483 chr7 159138663 90962162 0.5715905882657818 6.300043453438422 chr8 146364022 48222271 0.3294680642214109 3.178043397050387 chr9 141213431 39848539 0.2821866073064962 2.353639986932593 chr10 135534747 30009048 0.22141221099560543 6.857591327224829 chr11 135006516 43159811 0.31968687348394353 3.0413666577735423 chr12 133851895 46288220 0.3458166953855976 2.1617514550700876 chr13 115169878 32030754 0.278117460539465 2.2421935006606226 chr14 107349540 41078687 0.3826629066132934 29.90515643864879 chr15 102531392 15271621 0.14894580773857044 5.163620861222047 chr16 90354753 19068188 0.2110369113620398 10.31126661730711 chr17 81195210 12422901 0.1530004171428339 2.9728175191260107 chr18 78077248 30404815 0.3894196552624396 5.734794057851298 chr19 59128983 11269136 0.1905856557688469 6.415896920504868 chr20 63025520 15537098 0.24652074270866786 7.122834132096368 chr21 48129895 16082413 0.3341460229655602 2.0263550976771287 chr22 51304566 3263745 0.0636150981181675 1.29502904997266 chrMT 16571 10915 0.6586808279524471 0.9830442337531689 chrX 155270560 31777373 0.2046580691149694 9.004986848509594 chrY 59373566 4114459 0.06929782523084431 0.6397171000963388