BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779341.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 = 127,455,246 number of mapped reads = 123,965,328 (97.26%) number of supplementary alignments = 434,745 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 62,518,130 number of mapped paired reads (second in pair) = 61,447,198 number of mapped paired reads (both in pair) = 122,333,340 number of mapped paired reads (singletons) = 1,631,988 number of mapped bases = 12,284,709,342 bp number of sequenced bases = 12,281,919,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,778,134 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 49,516.6883 std insert size = 2,199,584.716 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 53.94 >>>>>>> ACTG content number of A's = 3,637,962,010 bp (29.62%) number of C's = 2,493,524,270 bp (20.3%) number of T's = 3,621,161,372 bp (29.48%) number of G's = 2,528,472,642 bp (20.59%) number of N's = 799,432 bp (0.01%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 44,731,747 number of insertions = 1,214,149 mapped reads with insertion percentage = 0.96% number of deletions = 1,264,638 mapped reads with deletion percentage = 1% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 3.9683X std coverageData = 5.7129X There is a 83.03% of reference with a coverageData >= 1X There is a 70.95% of reference with a coverageData >= 2X There is a 57.63% of reference with a coverageData >= 3X There is a 45.17% of reference with a coverageData >= 4X There is a 34.54% of reference with a coverageData >= 5X There is a 26% of reference with a coverageData >= 6X There is a 19.4% of reference with a coverageData >= 7X There is a 14.41% of reference with a coverageData >= 8X There is a 10.69% of reference with a coverageData >= 9X There is a 7.95% of reference with a coverageData >= 10X There is a 5.93% of reference with a coverageData >= 11X There is a 4.44% of reference with a coverageData >= 12X There is a 3.34% of reference with a coverageData >= 13X There is a 2.53% of reference with a coverageData >= 14X There is a 1.93% of reference with a coverageData >= 15X There is a 1.49% of reference with a coverageData >= 16X There is a 1.15% of reference with a coverageData >= 17X There is a 0.9% of reference with a coverageData >= 18X There is a 0.71% of reference with a coverageData >= 19X There is a 0.56% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.36% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% 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 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 989798860 3.971098872407624 7.171304328848775 chr2 243199373 1022049202 4.202515777045198 12.3572685257225 chr3 198022430 844677910 4.265566835029749 3.688015610108536 chr4 191154276 779668927 4.078741754121158 4.151591839227287 chr5 180915260 748575192 4.137711722051528 3.552077922757264 chr6 171115067 722271899 4.220971955672378 4.295580493666579 chr7 159138663 634707701 3.9883940774342186 4.265213784452557 chr8 146364022 611282461 4.176453015208888 3.7579056272699445 chr9 141213431 503374858 3.5646386780305623 4.830116960815485 chr10 135534747 693540060 5.117064629928442 7.125117176750297 chr11 135006516 562421089 4.165881067547881 3.924649715423147 chr12 133851895 650880338 4.862690498330263 4.813913982629098 chr13 115169878 384099271 3.3350670997498146 3.442966543479673 chr14 107349540 369589471 3.442860314073074 3.676302900919485 chr15 102531392 351285002 3.42612145556358 3.783072161491238 chr16 90354753 304772892 3.3730698372890244 3.7633383190983185 chr17 81195210 285388637 3.5148457279684355 4.2622822838327385 chr18 78077248 314521841 4.028341790427859 5.0823232181089 chr19 59128983 189546575 3.2056457828811293 5.0118540998490255 chr20 63025520 247190266 3.922066267759473 4.281268393543138 chr21 48129895 146856686 3.0512571448576815 5.747256155873661 chr22 51304566 119216422 2.3237000387061064 3.2684702861389137 chrMT 16571 2202282 132.89976464908574 33.31718490346159 chrX 155270560 794848199 5.119117229950095 4.47548854666046 chrY 59373566 11943301 0.20115519084705136 2.284553674114435