BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781913.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 44,904,082 number of mapped reads = 44,061,439 (98.12%) number of supplementary alignments = 155,367 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,216,093 number of mapped paired reads (second in pair) = 21,845,346 number of mapped paired reads (both in pair) = 43,552,712 number of mapped paired reads (singletons) = 508,727 number of mapped bases = 4,375,698,603 bp number of sequenced bases = 4,374,620,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,214,880 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 48,644.0962 std insert size = 2,123,102.581 median insert size = 277 >>>>>>> Mapping quality mean mapping quality = 53.9903 >>>>>>> ACTG content number of A's = 1,315,054,275 bp (30.06%) number of C's = 866,863,369 bp (19.82%) number of T's = 1,312,912,962 bp (30.01%) number of G's = 879,024,337 bp (20.09%) number of N's = 765,606 bp (0.02%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 16,363,545 number of insertions = 499,816 mapped reads with insertion percentage = 1.12% number of deletions = 483,297 mapped reads with deletion percentage = 1.08% homopolymer indels = 48.65% >>>>>>> Coverage mean coverageData = 1.4135X std coverageData = 2.0953X There is a 59.21% of reference with a coverageData >= 1X There is a 34.85% of reference with a coverageData >= 2X There is a 19.75% of reference with a coverageData >= 3X There is a 11.14% of reference with a coverageData >= 4X There is a 6.36% of reference with a coverageData >= 5X There is a 3.7% of reference with a coverageData >= 6X There is a 2.2% of reference with a coverageData >= 7X There is a 1.34% of reference with a coverageData >= 8X There is a 0.83% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% 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 338635673 1.3586151626879999 2.3152662006963545 chr2 243199373 355806488 1.4630238705426268 2.9620473264185154 chr3 198022430 298570844 1.507762751926638 1.822724505841308 chr4 191154276 282725218 1.4790420801258979 1.8528656720687728 chr5 180915260 264690831 1.4630652549707526 1.7662941418134586 chr6 171115067 258344575 1.5097710536501148 1.9199052312569929 chr7 159138663 222583335 1.3986754117696716 1.870512452622039 chr8 146364022 214499499 1.465520666000829 1.823576435271354 chr9 141213431 173891698 1.2314104739796317 1.9488024302899758 chr10 135534747 234547786 1.7305361996949757 2.7346039484792977 chr11 135006516 194884481 1.4435190742941622 1.8364198367966154 chr12 133851895 287292107 2.1463432176287083 2.5943215895948772 chr13 115169878 133794413 1.1617135949384265 1.6252830791455497 chr14 107349540 129898311 1.2100500011457898 1.724639792736239 chr15 102531392 117246259 1.143515724432962 1.6989564137470983 chr16 90354753 150238095 1.6627580731696538 2.21152381577558 chr17 81195210 91255110 1.1238977028324701 1.6814141463032692 chr18 78077248 107981663 1.383010617894729 1.8456137832949677 chr19 59128983 60000207 1.0147342970536124 1.867274360940814 chr20 63025520 80786988 1.2818139064937504 1.9430485631510355 chr21 48129895 50020756 1.039286622171106 2.006357721502683 chr22 51304566 37726370 0.7353413729296531 1.3929262467818455 chrMT 16571 92070 5.556091967895721 2.9535180208528415 chrX 155270560 286572999 1.8456364104051663 2.174899358871104 chrY 59373566 3612827 0.060849082232992374 0.6678085154159452