BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781854.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 = 349,553,126 number of mapped reads = 340,620,771 (97.44%) number of supplementary alignments = 863,697 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,227,299 number of mapped paired reads (second in pair) = 169,393,472 number of mapped paired reads (both in pair) = 336,662,692 number of mapped paired reads (singletons) = 3,958,079 number of mapped bases = 33,823,579,020 bp number of sequenced bases = 33,817,023,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,498,440 duplication rate = 11.45% >>>>>>> Insert size mean insert size = 24,529.6046 std insert size = 1,517,278.8858 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 53.9833 >>>>>>> ACTG content number of A's = 10,002,053,078 bp (29.58%) number of C's = 6,899,263,097 bp (20.4%) number of T's = 9,934,791,128 bp (29.38%) number of G's = 6,972,287,965 bp (20.62%) number of N's = 8,627,966 bp (0.03%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 139,412,878 number of insertions = 3,414,559 mapped reads with insertion percentage = 0.99% number of deletions = 2,878,865 mapped reads with deletion percentage = 0.83% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 10.926X std coverageData = 12.9033X There is a 88.58% of reference with a coverageData >= 1X There is a 84.56% of reference with a coverageData >= 2X There is a 79.62% of reference with a coverageData >= 3X There is a 74.17% of reference with a coverageData >= 4X There is a 68.48% of reference with a coverageData >= 5X There is a 62.79% of reference with a coverageData >= 6X There is a 57.27% of reference with a coverageData >= 7X There is a 52.02% of reference with a coverageData >= 8X There is a 47.12% of reference with a coverageData >= 9X There is a 42.59% of reference with a coverageData >= 10X There is a 38.45% of reference with a coverageData >= 11X There is a 34.69% of reference with a coverageData >= 12X There is a 31.29% of reference with a coverageData >= 13X There is a 28.23% of reference with a coverageData >= 14X There is a 25.48% of reference with a coverageData >= 15X There is a 23.01% of reference with a coverageData >= 16X There is a 20.8% of reference with a coverageData >= 17X There is a 18.82% of reference with a coverageData >= 18X There is a 17.05% of reference with a coverageData >= 19X There is a 15.46% of reference with a coverageData >= 20X There is a 14.03% of reference with a coverageData >= 21X There is a 12.75% of reference with a coverageData >= 22X There is a 11.6% of reference with a coverageData >= 23X There is a 10.57% of reference with a coverageData >= 24X There is a 9.64% of reference with a coverageData >= 25X There is a 8.81% of reference with a coverageData >= 26X There is a 8.05% of reference with a coverageData >= 27X There is a 7.37% of reference with a coverageData >= 28X There is a 6.76% of reference with a coverageData >= 29X There is a 6.2% of reference with a coverageData >= 30X There is a 5.69% of reference with a coverageData >= 31X There is a 5.23% of reference with a coverageData >= 32X There is a 4.82% of reference with a coverageData >= 33X There is a 4.44% of reference with a coverageData >= 34X There is a 4.09% of reference with a coverageData >= 35X There is a 3.78% of reference with a coverageData >= 36X There is a 3.5% of reference with a coverageData >= 37X There is a 3.23% of reference with a coverageData >= 38X There is a 3% of reference with a coverageData >= 39X There is a 2.78% of reference with a coverageData >= 40X There is a 2.58% of reference with a coverageData >= 41X There is a 2.39% of reference with a coverageData >= 42X There is a 2.22% of reference with a coverageData >= 43X There is a 2.07% of reference with a coverageData >= 44X There is a 1.93% of reference with a coverageData >= 45X There is a 1.79% of reference with a coverageData >= 46X There is a 1.67% of reference with a coverageData >= 47X There is a 1.56% of reference with a coverageData >= 48X There is a 1.46% of reference with a coverageData >= 49X There is a 1.36% of reference with a coverageData >= 50X There is a 1.28% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2767837294 11.104635498581166 16.288120533239244 chr2 243199373 2863270613 11.773347018456334 13.336551910661065 chr3 198022430 1387158259 7.005056240346106 7.809005545371874 chr4 191154276 2255604880 11.799918511893503 11.530069371261877 chr5 180915260 2130484453 11.77614565515369 10.754941112963925 chr6 171115067 2055734860 12.013757152080593 11.774161057799752 chr7 159138663 1791146733 11.25525814553312 12.412508460193022 chr8 146364022 1722113043 11.765958734039161 11.153914561968918 chr9 141213431 1392921940 9.863947997977615 13.199299176765074 chr10 135534747 1915133171 14.130200656219914 17.96436389348234 chr11 135006516 1572648885 11.64868875662268 11.733318106154018 chr12 133851895 2339054616 17.474945842193716 16.175540429100867 chr13 115169878 1081502627 9.390499024406365 10.168874994167345 chr14 107349540 1028308723 9.57906967277177 10.97924787573053 chr15 102531392 962473659 9.387111988102141 11.082627528514957 chr16 90354753 791396396 8.758768849713972 10.855733158556767 chr17 81195210 739923377 9.112894430595105 10.712709568580395 chr18 78077248 870094195 11.144017204602294 12.049354404379173 chr19 59128983 466980404 7.8976566195971944 11.612460388354759 chr20 63025520 649789648 10.309945050830203 12.857621593871215 chr21 48129895 412279565 8.565976821682241 14.808426749111252 chr22 51304566 310835121 6.058624899000217 9.354462498708312 chrMT 16571 429959 25.946472753605697 9.32789890054321 chrX 155270560 2286781942 14.727723929120884 14.371690882624431 chrY 59373566 29674657 0.49979576769904643 5.242455307379191