BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695989.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 14,758,276 number of mapped reads = 13,457,012 (91.18%) number of supplementary alignments = 221,025 (1.5%) number of secondary alignments = 0 number of mapped bases = 2,000,771,778 bp number of sequenced bases = 1,986,892,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,994,880 duplication rate = 19.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.9848 >>>>>>> ACTG content number of A's = 566,737,185 bp (28.52%) number of C's = 426,571,337 bp (21.47%) number of T's = 563,991,828 bp (28.39%) number of G's = 429,592,328 bp (21.62%) number of N's = 0 bp (0%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0165 number of mismatches = 21,028,217 number of insertions = 10,951,248 mapped reads with insertion percentage = 45.99% number of deletions = 12,483,851 mapped reads with deletion percentage = 52.57% homopolymer indels = 37.61% >>>>>>> Coverage mean coverageData = 0.6463X std coverageData = 1.7498X There is a 25.3% of reference with a coverageData >= 1X There is a 13.79% of reference with a coverageData >= 2X There is a 8.1% of reference with a coverageData >= 3X There is a 5.06% of reference with a coverageData >= 4X There is a 3.3% of reference with a coverageData >= 5X There is a 2.24% of reference with a coverageData >= 6X There is a 1.56% of reference with a coverageData >= 7X There is a 1.11% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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% 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 176695348 0.7089063501270073 2.0007018105815497 chr2 243199373 248060541 1.0199884067957692 2.1782068389983062 chr3 198022430 125330217 0.6329091961956027 1.5846028637444987 chr4 191154276 105321380 0.55097579925442 1.5192821233506926 chr5 180915260 123467862 0.6824623970360488 1.7878539372913593 chr6 171115067 108048659 0.6314386038255766 1.6867467863155043 chr7 159138663 102081604 0.6414632501970938 1.6510328666713492 chr8 146364022 98807640 0.6750814759654528 1.6494490414658913 chr9 141213431 76056669 0.5385937333397133 1.5400926466265268 chr10 135534747 98279729 0.7251257052186034 1.9426606538570037 chr11 135006516 92630732 0.6861204536231421 1.7308121524586615 chr12 133851895 90485316 0.6760107206550942 1.664191604382251 chr13 115169878 56995858 0.49488511223394716 1.4595688653101206 chr14 107349540 64702008 0.6027227317415612 1.6452989347265883 chr15 102531392 63048146 0.6149155372824744 1.7178743197063682 chr16 90354753 66268364 0.7334242173181525 2.010411977727655 chr17 81195210 63732413 0.7849282365302092 2.118879475880775 chr18 78077248 50755132 0.6500630247623482 1.842391138482326 chr19 59128983 37703462 0.6376477335996122 1.956572206141963 chr20 63025520 44770351 0.7103527428254459 1.8301859344895912 chr21 48129895 22495995 0.46740170532264824 1.5637383870199684 chr22 51304566 23094883 0.45015258485960097 1.462952056977626 chrMT 16571 692364 41.78166676724398 26.519142829529805 chrX 155270560 51680768 0.3328433155647793 1.1361967966161606 chrY 59373566 9566337 0.16112114606692143 0.9607876130945815