BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714122.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 617,818 number of mapped reads = 538,491 (87.16%) number of supplementary alignments = 16,507 (2.67%) number of secondary alignments = 0 number of mapped bases = 70,330,179 bp number of sequenced bases = 68,715,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 486,698 duplication rate = 43.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3463 >>>>>>> ACTG content number of A's = 18,441,580 bp (26.84%) number of C's = 15,442,058 bp (22.47%) number of T's = 17,410,771 bp (25.34%) number of G's = 17,420,292 bp (25.35%) number of N's = 416 bp (0%) GC percentage = 47.82% >>>>>>> Mismatches and indels general error rate = 0.0448 number of mismatches = 2,867,977 number of insertions = 76,790 mapped reads with insertion percentage = 13.8% number of deletions = 251,940 mapped reads with deletion percentage = 44.43% homopolymer indels = 29.07% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 6.6679X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6014449 0.02413012644008618 5.960400663821551 chr2 243199373 8474783 0.03484705941244347 9.919347587596004 chr3 198022430 2307478 0.011652609252396307 2.227370374393919 chr4 191154276 2543805 0.013307601866044577 3.6684670271217903 chr5 180915260 3108928 0.017184443147581913 3.4027506973563204 chr6 171115067 2435081 0.014230663860827638 2.653906318104512 chr7 159138663 1816363 0.01141371283231153 1.8388297750224698 chr8 146364022 2545674 0.017392757900572042 4.257626613199322 chr9 141213431 3399228 0.02407156299459929 6.41595949158294 chr10 135534747 2968194 0.021899874871201847 3.474804770308264 chr11 135006516 3118875 0.02310166273752298 3.692459714140572 chr12 133851895 4371461 0.03265893994253873 7.795034630874146 chr13 115169878 2611351 0.022673906105900365 8.582464906002823 chr14 107349540 4396739 0.040957222546086365 21.916013105846204 chr15 102531392 2261860 0.02206017060609106 3.8757361266174803 chr16 90354753 1098762 0.01216053349180203 1.6352826960161504 chr17 81195210 3098892 0.03816594599607538 8.205811545498575 chr18 78077248 1850972 0.023706931883664753 4.652496446546585 chr19 59128983 2019184 0.03414880313432754 4.729861809281491 chr20 63025520 2114754 0.03355393180413267 5.051004448242082 chr21 48129895 674362 0.014011291734586165 2.4588708971791924 chr22 51304566 413433 0.008058405561797365 1.1149534145244937 chrMT 16571 149035 8.993723975620059 76.19444504180007 chrX 155270560 5970775 0.03845400570462295 5.2793500011719665 chrY 59373566 565741 0.009528499601994598 3.4050086853367136