BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779429.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 = 12,714,996 number of mapped reads = 11,321,554 (89.04%) number of supplementary alignments = 189,481 (1.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,687,398 number of mapped paired reads (second in pair) = 5,634,156 number of mapped paired reads (both in pair) = 11,216,244 number of mapped paired reads (singletons) = 105,310 number of mapped bases = 891,826,572 bp number of sequenced bases = 891,609,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,452,995 duplication rate = 38% >>>>>>> Insert size mean insert size = 99,278.2609 std insert size = 3,019,524.3395 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 50.1458 >>>>>>> ACTG content number of A's = 269,761,828 bp (30.26%) number of C's = 175,766,553 bp (19.71%) number of T's = 266,945,113 bp (29.94%) number of G's = 178,946,701 bp (20.07%) number of N's = 188,983 bp (0.02%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 4,403,693 number of insertions = 90,905 mapped reads with insertion percentage = 0.8% number of deletions = 111,774 mapped reads with deletion percentage = 0.98% homopolymer indels = 50.68% >>>>>>> Coverage mean coverageData = 0.2881X std coverageData = 45.1661X There is a 0.7% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% 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 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% 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 98922001 0.3968776511092424 53.140230753331295 chr2 243199373 89719117 0.36891179402835056 41.78448355085602 chr3 198022430 34957125 0.1765311384169965 21.502393112365965 chr4 191154276 64564483 0.3377611233765966 75.9785323108433 chr5 180915260 67985496 0.37578640961519777 55.760046420111856 chr6 171115067 20361796 0.11899475807118727 27.39113573183606 chr7 159138663 54686371 0.34363975396726815 29.497185328347935 chr8 146364022 20554613 0.140434874084015 20.06275902694023 chr9 141213431 79737682 0.5646607510017939 63.61696405046625 chr10 135534747 3764962 0.027778574006560842 3.8771728071379847 chr11 135006516 54364655 0.40268171204418013 49.767111777104176 chr12 133851895 75797030 0.566275359792254 58.95179064084713 chr13 115169878 27714546 0.2406405779122211 33.54554316193768 chr14 107349540 10509577 0.09790053129244895 15.354009158799307 chr15 102531392 28472230 0.27769280651139505 34.8263401258649 chr16 90354753 36211896 0.4007746664970685 53.961934330672726 chr17 81195210 1169577 0.014404507359485862 1.1575439149607476 chr18 78077248 14503745 0.18576147817095193 24.97040526216527 chr19 59128983 14113054 0.23868250871150617 48.60895086837393 chr20 63025520 4171352 0.0661851262790057 8.750903651498945 chr21 48129895 39529162 0.8213016463052745 71.6154867484014 chr22 51304566 1603761 0.031259615372245815 5.392628251653596 chrMT 16571 239722 14.46635688854022 7.550089610256276 chrX 155270560 30391025 0.19572947376502023 62.33975916607708 chrY 59373566 17781594 0.29948671097168056 49.03178348364955