BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504738.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,130,902 number of mapped reads = 1,893,638 (88.87%) number of secondary alignments = 0 number of mapped bases = 60,590,606 bp number of sequenced bases = 60,590,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,877 duplication rate = 8.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.0721 >>>>>>> ACTG content number of A's = 17,510,663 bp (28.9%) number of C's = 12,167,741 bp (20.08%) number of T's = 18,563,262 bp (30.64%) number of G's = 12,348,853 bp (20.38%) number of N's = 87 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 27,943 >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.852X There is a 1.03% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 4276460 0.017157269188910064 0.26273916080997567 chr2 243199373 4316954 0.017750678987153476 0.42526508049265016 chr3 198022430 4322518 0.021828426204041632 0.5067980950798835 chr4 191154276 3663290 0.01916404946128435 0.4643802324986087 chr5 180915260 3370554 0.018630567703354597 0.2399495761799957 chr6 171115067 4033532 0.02357204465226899 0.39930914187808175 chr7 159138663 3601410 0.022630641304307048 0.9595837696708843 chr8 146364022 2627450 0.01795147444089778 0.28814121278103694 chr9 141213431 2569564 0.018196314485128543 0.557482232295406 chr10 135534747 2149142 0.015856760333200756 0.24348308364401672 chr11 135006516 2330578 0.01726270752739075 0.2517221430179518 chr12 133851895 2477534 0.018509517552964042 0.3033737040094511 chr13 115169878 5254246 0.04562170327210037 3.5277288722509517 chr14 107349540 1530350 0.014255766722428433 0.21654051075138264 chr15 102531392 1685088 0.01643484953369208 0.3031899050758454 chr16 90354753 930684 0.01030033251266815 0.19128707248803078 chr17 81195210 966122 0.011898756096572692 0.2191902496638536 chr18 78077248 1647808 0.02110484221984873 0.4105854290355864 chr19 59128983 644138 0.010893777760392057 0.18180338127390458 chr20 63025520 2656050 0.04214245277151224 2.1812614156540198 chr21 48129895 425644 0.008843651123693496 0.13575084483991526 chr22 51304566 368438 0.007181388104910584 0.12408839495228596 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 4592440 0.029577017046888993 0.5825287563746762 chrY 59373566 150580 0.002536145462443674 0.05853208136711839