BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717006.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,771,838 number of mapped reads = 1,603,541 (90.5%) number of supplementary alignments = 7,592 (0.43%) number of secondary alignments = 0 number of mapped bases = 93,126,852 bp number of sequenced bases = 93,101,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,795 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.978 >>>>>>> ACTG content number of A's = 23,840,099 bp (25.61%) number of C's = 17,129,326 bp (18.4%) number of T's = 28,578,113 bp (30.7%) number of G's = 23,551,527 bp (25.3%) number of N's = 2,187 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 456,160 number of insertions = 5,816 mapped reads with insertion percentage = 0.36% number of deletions = 15,206 mapped reads with deletion percentage = 0.94% homopolymer indels = 40.23% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2633X There is a 2.68% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7579296 0.030408333466097965 0.4841120517889158 chr2 243199373 7891772 0.03244980405438792 0.27728444430964944 chr3 198022430 6160838 0.031111818999494147 0.19308025514264082 chr4 191154276 5926167 0.031002011171332625 0.20997579459296353 chr5 180915260 5601507 0.03096204819869811 0.19415092455024952 chr6 171115067 5301624 0.030982800596980744 0.20495169893952553 chr7 159138663 5016000 0.03151968167534498 0.2694990392114584 chr8 146364022 4724924 0.03228200438493006 0.258466153923115 chr9 141213431 3930699 0.02783516392289909 0.24746853928675536 chr10 135534747 4417630 0.03259407714834927 0.24555136283479315 chr11 135006516 4230838 0.03133802815858162 0.24636845250897477 chr12 133851895 4212591 0.0314720310833104 0.19822542518571062 chr13 115169878 2915678 0.025316324464631283 0.17299310804792528 chr14 107349540 2825414 0.02631975879915275 0.18457092401156158 chr15 102531392 2729910 0.026625113994355992 0.17828033180200803 chr16 90354753 2758432 0.030528908645237513 0.2081984693868149 chr17 81195210 2589625 0.031893814918392355 0.20681018058238526 chr18 78077248 2504132 0.03207249312885618 0.4721357705233449 chr19 59128983 1889708 0.03195908172477785 0.3210208168014017 chr20 63025520 2040727 0.032379375846482504 0.2030798758928105 chr21 48129895 1247700 0.025923596966085215 0.19331317843772303 chr22 51304566 1150039 0.022415919082133938 0.16379965712411107 chrMT 16571 9389 0.5665922394544687 0.9098282407468405 chrX 155270560 5193846 0.03345029476289646 0.22910011385165885 chrY 59373566 278366 0.004688382705529259 0.1166431076837846