BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008704.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,649,852 number of mapped reads = 1,252,773 (75.93%) number of supplementary alignments = 6,755 (0.41%) number of secondary alignments = 0 number of mapped bases = 83,710,526 bp number of sequenced bases = 83,664,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,427 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7983 >>>>>>> ACTG content number of A's = 25,318,063 bp (30.26%) number of C's = 14,592,978 bp (17.44%) number of T's = 24,843,997 bp (29.69%) number of G's = 18,892,980 bp (22.58%) number of N's = 16,820 bp (0.02%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 758,992 number of insertions = 5,885 mapped reads with insertion percentage = 0.47% number of deletions = 27,115 mapped reads with deletion percentage = 2.14% homopolymer indels = 44.77% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2238X There is a 2.54% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 7357821 0.029519769982839884 0.36254982740994696 chr2 243199373 6543080 0.02690418120444743 0.2550830363018759 chr3 198022430 4823176 0.02435671554984958 0.1664733509829214 chr4 191154276 4678405 0.02447449828430728 0.16563837748711435 chr5 180915260 4615753 0.02551334254501251 0.1648052270216535 chr6 171115067 4301774 0.025139656462864254 0.17863797382769714 chr7 159138663 4394128 0.027611944936347742 0.21896040324019284 chr8 146364022 6999423 0.04782201871987366 0.277535923091616 chr9 141213431 2986594 0.02114950383154418 0.1913935533201091 chr10 135534747 4949012 0.03651471013554922 0.33526511514517476 chr11 135006516 3471933 0.02571678095892794 0.20131333350427968 chr12 133851895 4197325 0.03135797965355664 0.1840077221968294 chr13 115169878 2446717 0.021244417746105453 0.1496785985742879 chr14 107349540 3618444 0.033707121614121496 0.19396191625074308 chr15 102531392 1157358 0.011287840508397663 0.10956363668028428 chr16 90354753 1948182 0.02156147778966315 0.16607355594948278 chr17 81195210 2626985 0.03235394058344082 0.2104050627214615 chr18 78077248 1323339 0.016949098923158767 0.30360520993002044 chr19 59128983 1446451 0.024462639582351686 0.22580056716378746 chr20 63025520 2157385 0.03423034034467308 0.1942941605927857 chr21 48129895 1111634 0.023096539063714974 0.16229680978318267 chr22 51304566 1046164 0.020391245488754355 0.14759322475882483 chrMT 16571 14243 0.8595136081105546 1.0366401959206697 chrX 155270560 5287381 0.034052694857286535 0.2036958635637331 chrY 59373566 207819 0.0035001940088961476 0.08855518255337588