BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080802.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,094,650 number of mapped reads = 2,567,754 (82.97%) number of supplementary alignments = 29,675 (0.96%) number of secondary alignments = 0 number of mapped bases = 180,852,723 bp number of sequenced bases = 180,787,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,684 duplication rate = 5.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0125 >>>>>>> ACTG content number of A's = 55,187,524 bp (30.53%) number of C's = 33,011,856 bp (18.26%) number of T's = 56,830,527 bp (31.44%) number of G's = 35,730,694 bp (19.76%) number of N's = 26,419 bp (0.01%) GC percentage = 38.02% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,404,449 number of insertions = 14,018 mapped reads with insertion percentage = 0.54% number of deletions = 36,775 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.6391X There is a 3.18% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% 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% of reference with a coverageData >= 11X There is a 0% 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 12439451 0.04990740223672301 0.4517127008972275 chr2 243199373 15322318 0.06300311473253675 0.461717090704162 chr3 198022430 13218614 0.06675311478603711 0.424280836088661 chr4 191154276 13992576 0.0732004341875146 0.4524272499131192 chr5 180915260 11468611 0.0633921704559361 0.4134743321402251 chr6 171115067 11673410 0.06821965011415389 0.4492537886977921 chr7 159138663 10212630 0.06417441121771898 0.4609662894475181 chr8 146364022 9648484 0.0659211455667705 2.2497179675216756 chr9 141213431 6691086 0.04738278754802013 0.3939462078400771 chr10 135534747 8346927 0.06158514465666874 0.43606115281882246 chr11 135006516 8785056 0.06507134811182003 0.4342289685637226 chr12 133851895 8147103 0.06086654955464022 0.40219474785543163 chr13 115169878 5979066 0.051915189143466836 0.378612581512332 chr14 107349540 5285628 0.04923754680271569 0.3703895046957815 chr15 102531392 5303058 0.0517213108742345 0.3686237361822786 chr16 90354753 4540027 0.050246687077989134 0.364493807004034 chr17 81195210 4273848 0.05263670110589036 0.3710806002616362 chr18 78077248 4838646 0.06197254800783962 0.5678368620535216 chr19 59128983 2154446 0.03643637841699391 0.34726180258594136 chr20 63025520 2758508 0.04376811171093868 0.3409899451041739 chr21 48129895 2545166 0.05288118746155586 0.38320692263107675 chr22 51304566 1550511 0.030221696057228124 0.26932536140749985 chrMT 16571 17200 1.0379578782209884 1.5649246699953223 chrX 155270560 11217021 0.0722417759039447 0.44654616631347827 chrY 59373566 443332 0.0074668245461288274 0.17251360330728968