BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438300.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 778,937,652 number of mapped reads = 774,938,336 (99.49%) number of supplementary alignments = 21,453,715 (2.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 387,622,105 number of mapped paired reads (second in pair) = 387,316,231 number of mapped paired reads (both in pair) = 772,473,878 number of mapped paired reads (singletons) = 2,464,458 number of mapped bases = 109,885,272,293 bp number of sequenced bases = 109,849,867,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 317,646,739 duplication rate = 35.93% >>>>>>> Insert size mean insert size = 104,440.3128 std insert size = 3,123,967.7694 median insert size = 454 >>>>>>> Mapping quality mean mapping quality = 54.2715 >>>>>>> ACTG content number of A's = 33,771,646,390 bp (30.74%) number of C's = 20,806,433,729 bp (18.94%) number of T's = 31,816,781,453 bp (28.96%) number of G's = 23,454,804,092 bp (21.35%) number of N's = 202,247 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 599,185,493 number of insertions = 14,645,391 mapped reads with insertion percentage = 1.84% number of deletions = 12,954,506 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 35.4962X std coverageData = 128.4346X There is a 90.93% of reference with a coverageData >= 1X There is a 90.22% of reference with a coverageData >= 2X There is a 89.48% of reference with a coverageData >= 3X There is a 88.7% of reference with a coverageData >= 4X There is a 87.84% of reference with a coverageData >= 5X There is a 86.92% of reference with a coverageData >= 6X There is a 85.93% of reference with a coverageData >= 7X There is a 84.85% of reference with a coverageData >= 8X There is a 83.7% of reference with a coverageData >= 9X There is a 82.47% of reference with a coverageData >= 10X There is a 81.16% of reference with a coverageData >= 11X There is a 79.79% of reference with a coverageData >= 12X There is a 78.35% of reference with a coverageData >= 13X There is a 76.86% of reference with a coverageData >= 14X There is a 75.3% of reference with a coverageData >= 15X There is a 73.7% of reference with a coverageData >= 16X There is a 72.06% of reference with a coverageData >= 17X There is a 70.39% of reference with a coverageData >= 18X There is a 68.68% of reference with a coverageData >= 19X There is a 66.96% of reference with a coverageData >= 20X There is a 65.21% of reference with a coverageData >= 21X There is a 63.46% of reference with a coverageData >= 22X There is a 61.71% of reference with a coverageData >= 23X There is a 59.95% of reference with a coverageData >= 24X There is a 58.2% of reference with a coverageData >= 25X There is a 56.47% of reference with a coverageData >= 26X There is a 54.74% of reference with a coverageData >= 27X There is a 53.04% of reference with a coverageData >= 28X There is a 51.36% of reference with a coverageData >= 29X There is a 49.71% of reference with a coverageData >= 30X There is a 48.08% of reference with a coverageData >= 31X There is a 46.48% of reference with a coverageData >= 32X There is a 44.91% of reference with a coverageData >= 33X There is a 43.38% of reference with a coverageData >= 34X There is a 41.88% of reference with a coverageData >= 35X There is a 40.42% of reference with a coverageData >= 36X There is a 39% of reference with a coverageData >= 37X There is a 37.61% of reference with a coverageData >= 38X There is a 36.26% of reference with a coverageData >= 39X There is a 34.95% of reference with a coverageData >= 40X There is a 33.68% of reference with a coverageData >= 41X There is a 32.45% of reference with a coverageData >= 42X There is a 31.25% of reference with a coverageData >= 43X There is a 30.1% of reference with a coverageData >= 44X There is a 28.97% of reference with a coverageData >= 45X There is a 27.89% of reference with a coverageData >= 46X There is a 26.84% of reference with a coverageData >= 47X There is a 25.83% of reference with a coverageData >= 48X There is a 24.85% of reference with a coverageData >= 49X There is a 23.91% of reference with a coverageData >= 50X There is a 23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8646160993 34.688623676488255 44.31530395878399 chr2 243199373 9452295633 38.86644737772412 235.05843103577604 chr3 198022430 7747838956 39.12606746619562 28.386348321292136 chr4 191154276 7565224301 39.57653712648311 38.46445903398652 chr5 180915260 6915576473 38.22550111582627 28.40214271801106 chr6 171115067 6587593414 38.49803251983649 35.078542227034454 chr7 159138663 5828127183 36.622949276631786 31.044894804510673 chr8 146364022 5586475143 38.16836314459847 32.35847223732952 chr9 141213431 4549113581 32.21445402739347 58.30458391541411 chr10 135534747 4925085173 36.338173656678606 88.73921548766903 chr11 135006516 4963023255 36.76136087387071 32.218452283777154 chr12 133851895 4927021161 36.80949874486274 30.359795083801988 chr13 115169878 3788300682 32.89315529187241 29.497747843741084 chr14 107349540 3322530948 30.95058393356879 30.160839621160157 chr15 102531392 3022397238 29.477774358120488 29.268766961400715 chr16 90354753 3552046938 39.31223117836424 113.51818686355669 chr17 81195210 2399986962 29.558233324354973 49.89028489040742 chr18 78077248 2945945748 37.73116783009565 68.29194270730115 chr19 59128983 1468662974 24.83829248340023 31.143970705054823 chr20 63025520 2095338598 33.245875607214344 32.64097090188918 chr21 48129895 1399674226 29.081181789405523 46.42263626892622 chr22 51304566 965748756 18.82383638134664 25.895854811833864 chrMT 16571 678460622 40942.648120210004 15244.256285133406 chrX 155270560 6417428191 41.33061792911676 32.14368528853315 chrY 59373566 135215144 2.2773626903258597 38.446434754880926