BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264623.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,531,466,718 number of mapped reads = 1,521,652,562 (99.36%) number of supplementary alignments = 8,841,737 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 763,358,148 number of mapped paired reads (second in pair) = 758,294,414 number of mapped paired reads (both in pair) = 1,515,288,608 number of mapped paired reads (singletons) = 6,363,954 number of mapped bases = 152,747,303,232 bp number of sequenced bases = 152,712,445,283 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 637,351,613 duplication rate = 41.75% >>>>>>> Insert size mean insert size = 68,703.1778 std insert size = 2,516,978.8831 median insert size = 303 >>>>>>> Mapping quality mean mapping quality = 54.5899 >>>>>>> ACTG content number of A's = 47,389,401,853 bp (31.03%) number of C's = 28,959,583,566 bp (18.96%) number of T's = 47,075,817,635 bp (30.83%) number of G's = 29,261,230,478 bp (19.16%) number of N's = 26,411,751 bp (0.02%) GC percentage = 38.12% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 562,699,824 number of insertions = 16,822,045 mapped reads with insertion percentage = 1.09% number of deletions = 15,617,909 mapped reads with deletion percentage = 1.01% homopolymer indels = 48.66% >>>>>>> Coverage mean coverageData = 49.3419X std coverageData = 50.153X There is a 90.72% of reference with a coverageData >= 1X There is a 89.48% of reference with a coverageData >= 2X There is a 88.25% of reference with a coverageData >= 3X There is a 87.03% of reference with a coverageData >= 4X There is a 85.8% of reference with a coverageData >= 5X There is a 84.58% of reference with a coverageData >= 6X There is a 83.35% of reference with a coverageData >= 7X There is a 82.13% of reference with a coverageData >= 8X There is a 80.92% of reference with a coverageData >= 9X There is a 79.7% of reference with a coverageData >= 10X There is a 78.49% of reference with a coverageData >= 11X There is a 77.29% of reference with a coverageData >= 12X There is a 76.1% of reference with a coverageData >= 13X There is a 74.9% of reference with a coverageData >= 14X There is a 73.72% of reference with a coverageData >= 15X There is a 72.54% of reference with a coverageData >= 16X There is a 71.37% of reference with a coverageData >= 17X There is a 70.21% of reference with a coverageData >= 18X There is a 69.05% of reference with a coverageData >= 19X There is a 67.91% of reference with a coverageData >= 20X There is a 66.77% of reference with a coverageData >= 21X There is a 65.64% of reference with a coverageData >= 22X There is a 64.53% of reference with a coverageData >= 23X There is a 63.42% of reference with a coverageData >= 24X There is a 62.32% of reference with a coverageData >= 25X There is a 61.24% of reference with a coverageData >= 26X There is a 60.16% of reference with a coverageData >= 27X There is a 59.09% of reference with a coverageData >= 28X There is a 58.04% of reference with a coverageData >= 29X There is a 57% of reference with a coverageData >= 30X There is a 55.96% of reference with a coverageData >= 31X There is a 54.94% of reference with a coverageData >= 32X There is a 53.93% of reference with a coverageData >= 33X There is a 52.94% of reference with a coverageData >= 34X There is a 51.95% of reference with a coverageData >= 35X There is a 50.98% of reference with a coverageData >= 36X There is a 50.02% of reference with a coverageData >= 37X There is a 49.08% of reference with a coverageData >= 38X There is a 48.14% of reference with a coverageData >= 39X There is a 47.22% of reference with a coverageData >= 40X There is a 46.31% of reference with a coverageData >= 41X There is a 45.42% of reference with a coverageData >= 42X There is a 44.53% of reference with a coverageData >= 43X There is a 43.66% of reference with a coverageData >= 44X There is a 42.81% of reference with a coverageData >= 45X There is a 41.97% of reference with a coverageData >= 46X There is a 41.13% of reference with a coverageData >= 47X There is a 40.32% of reference with a coverageData >= 48X There is a 39.51% of reference with a coverageData >= 49X There is a 38.72% of reference with a coverageData >= 50X There is a 37.94% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11839251300 47.499385367629635 51.27006699329572 chr2 243199373 13545189472 55.69582398553305 50.31031664283718 chr3 198022430 12216338584 61.691691107921464 50.972553969618495 chr4 191154276 12267642027 64.17665502287797 50.79244457250735 chr5 180915260 10663070404 58.939585328512365 50.33412610985751 chr6 171115067 10567808466 61.75849182234782 53.1630451707692 chr7 159138663 8509816727 53.47422534899643 51.698641214521636 chr8 146364022 8669667233 59.23359521371994 49.72635317574736 chr9 141213431 6426243707 45.507312310824034 52.39641882763944 chr10 135534747 6643892422 49.019845973519985 46.21611310671463 chr11 135006516 7078253056 52.42897354672866 50.712391091007895 chr12 133851895 7267896939 54.29805038621231 53.658112689628865 chr13 115169878 5944017030 51.61086503886025 52.20044414839006 chr14 107349540 4896109206 45.60903759811174 50.00688803330552 chr15 102531392 4083489671 39.82672615036768 49.19687040013965 chr16 90354753 2853885860 31.585342942611994 38.77858651220643 chr17 81195210 2517898595 31.01043269670711 40.7187721430184 chr18 78077248 4417682955 56.58092553415817 49.2581128492016 chr19 59128983 1119816109 18.938531531989987 27.40703908884675 chr20 63025520 2443821445 38.77510959052778 50.452883456026285 chr21 48129895 2005131025 41.66082275891107 54.287036443660384 chr22 51304566 778675496 15.17750868411985 26.118771432825962 chrMT 16571 69615 4.201013819322913 7.589272629959504 chrX 155270560 5272222506 33.955068533275075 34.91217453574245 chrY 59373566 719413382 12.116728545494471 27.142597040692117