BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818824.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,697,510 number of mapped reads = 1,655,465 (97.52%) number of supplementary alignments = 12,055 (0.71%) number of secondary alignments = 0 number of mapped bases = 112,464,329 bp number of sequenced bases = 112,419,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 715,834 duplication rate = 36.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7476 >>>>>>> ACTG content number of A's = 30,722,121 bp (27.33%) number of C's = 25,833,010 bp (22.98%) number of T's = 32,006,829 bp (28.47%) number of G's = 23,850,011 bp (21.22%) number of N's = 7,040 bp (0.01%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 569,710 number of insertions = 11,405 mapped reads with insertion percentage = 0.68% number of deletions = 28,172 mapped reads with deletion percentage = 1.69% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.4631X There is a 1.8% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9361102 0.03755698566544394 0.6336637341706056 chr2 243199373 9999421 0.04111614629861731 0.7349853189532949 chr3 198022430 7724844 0.03900994447952184 0.3525485178465765 chr4 191154276 7259168 0.037975441365486376 0.39315111830162636 chr5 180915260 6929111 0.03830031253306106 0.3613498617518706 chr6 171115067 6593884 0.0385347948348698 0.3809481966298273 chr7 159138663 6164570 0.03873709809915897 0.4143785653959698 chr8 146364022 5752623 0.03930353184746454 0.38922017526001695 chr9 141213431 4897263 0.034679866959680346 0.38275308933238383 chr10 135534747 5588934 0.04123617097245181 0.5049212326960327 chr11 135006516 5386448 0.039897689086354916 0.39575677006251925 chr12 133851895 5203861 0.03887775365451494 0.3690241560595014 chr13 115169878 3534487 0.03068933527914304 0.3104601060278699 chr14 107349540 3511772 0.0327134331455915 0.3562671766035496 chr15 102531392 3286176 0.03205043778202094 0.32411286926389965 chr16 90354753 3487564 0.03859856713901924 0.5151786205269409 chr17 81195210 2252666 0.027743828730783505 0.32568267621285263 chr18 78077248 3097707 0.039674899914505186 0.482227673828731 chr19 59128983 2360264 0.0399172094673098 0.5888744064420086 chr20 63025520 2526957 0.04009418724351659 0.3788461760251935 chr21 48129895 1533972 0.03187150107017686 0.32955302977030354 chr22 51304566 1436171 0.027993044517714075 0.3438954678000566 chrMT 16571 60938 3.6773882083157323 4.7661374283652735 chrX 155270560 3479899 0.022411840338567725 0.29771243368755557 chrY 59373566 1034527 0.017424033449498385 0.8636795567024842