BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008722.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 = 1,582,349 number of mapped reads = 1,023,667 (64.69%) number of supplementary alignments = 4,468 (0.28%) number of secondary alignments = 0 number of mapped bases = 64,864,765 bp number of sequenced bases = 64,828,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,350 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9679 >>>>>>> ACTG content number of A's = 18,727,050 bp (28.89%) number of C's = 11,017,342 bp (16.99%) number of T's = 19,873,186 bp (30.66%) number of G's = 15,194,258 bp (23.44%) number of N's = 16,318 bp (0.03%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 681,263 number of insertions = 5,564 mapped reads with insertion percentage = 0.54% number of deletions = 22,872 mapped reads with deletion percentage = 2.21% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.1946X There is a 1.92% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 6293544 0.02524986286794447 0.2861328033971972 chr2 243199373 7101490 0.02920028087407939 0.26837726968317954 chr3 198022430 3794065 0.019159773971059745 0.14865030438554858 chr4 191154276 4505939 0.023572263693436814 0.16838390602028275 chr5 180915260 3458071 0.019114313518936988 0.1475768531231367 chr6 171115067 2992233 0.017486671702615177 0.15147200776254263 chr7 159138663 3546443 0.02228523812594806 0.2239132209969719 chr8 146364022 4191062 0.028634509647459675 0.24641488286492286 chr9 141213431 2822376 0.019986597450493217 0.1947445731731573 chr10 135534747 3118212 0.02300673494450836 0.2094231978627321 chr11 135006516 2373821 0.01758301058594831 0.16197052179118274 chr12 133851895 2439827 0.01822781067089114 0.14597795011634696 chr13 115169878 2486779 0.021592269117451005 0.15653984807172422 chr14 107349540 1743914 0.016245193039485777 0.14112466518721206 chr15 102531392 1905022 0.018579890147204868 0.1474255411438368 chr16 90354753 1666451 0.018443423778713667 0.154181334016933 chr17 81195210 1699210 0.02092746604140811 0.16093362530740207 chr18 78077248 917237 0.011747814164761545 0.24977923885818518 chr19 59128983 919220 0.015546014041878583 0.18509590918085322 chr20 63025520 1385041 0.021975875803960047 0.1599529015448792 chr21 48129895 740567 0.01538684013335163 0.14102711222340084 chr22 51304566 495780 0.009663467380271767 0.1044307081702544 chrMT 16571 21703 1.309697664594774 1.459125569741526 chrX 155270560 4068244 0.026201000369934904 0.18077989040795628 chrY 59373566 178514 0.003006624193668947 0.07831327192566284