BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124782.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 315,306 number of mapped reads = 307,978 (97.68%) number of supplementary alignments = 45,077 (14.3%) number of secondary alignments = 0 number of mapped bases = 42,103,818 bp number of sequenced bases = 42,080,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,359 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.976 >>>>>>> ACTG content number of A's = 12,042,730 bp (28.62%) number of C's = 7,838,215 bp (18.63%) number of T's = 12,510,681 bp (29.73%) number of G's = 9,688,454 bp (23.02%) number of N's = 0 bp (0%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 567,830 number of insertions = 5,814 mapped reads with insertion percentage = 1.74% number of deletions = 11,655 mapped reads with deletion percentage = 3.63% homopolymer indels = 44.48% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 14.9121X There is a 0.63% of reference with a coverageData >= 1X There is a 0.02% 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 6773139 0.027174010531351895 18.806069278538924 chr2 243199373 2211071 0.009091598274803119 0.9826252666732379 chr3 198022430 1419864 0.007170218040451276 0.13362376744489227 chr4 191154276 1352270 0.0070742335892083315 0.13097620556618933 chr5 180915260 2752124 0.015212226984058724 9.365540291934106 chr6 171115067 1199949 0.007012526839614889 0.09175289649620097 chr7 159138663 1148552 0.007217303314908458 0.10016027661191919 chr8 146364022 1006161 0.006874373812985271 0.10881159652321507 chr9 141213431 935770 0.006626635960711131 0.12598043319838598 chr10 135534747 14511113 0.10706562945072676 65.62792336882757 chr11 135006516 989365 0.0073282759181786455 0.12381766493965134 chr12 133851895 920494 0.006876959044920507 0.1034209105840223 chr13 115169878 768315 0.006671145384038698 0.8177024279231275 chr14 107349540 630070 0.005869331158754849 0.08077057490276324 chr15 102531392 898675 0.008764876614568932 1.3127856744691764 chr16 90354753 730349 0.008083127624730489 0.19151772450960808 chr17 81195210 622763 0.007669947525229629 0.15879608885141702 chr18 78077248 578802 0.007413196735622649 0.3234128005631026 chr19 59128983 573675 0.009702094825476704 1.2283902421382062 chr20 63025520 475508 0.007544689833578525 0.09728065938790612 chr21 48129895 279946 0.0058164681223592946 0.09234645621388733 chr22 51304566 228351 0.004450890394433899 0.07744445296785561 chrMT 16571 83737 5.05322551445296 3.5274023287113714 chrX 155270560 648524 0.004176735113211416 0.09811725208666021 chrY 59373566 365231 0.006151407513572622 0.22283463084593633