BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716490.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 = 1,269,823 number of mapped reads = 1,044,411 (82.25%) number of supplementary alignments = 4,157 (0.33%) number of secondary alignments = 0 number of mapped bases = 58,888,210 bp number of sequenced bases = 58,869,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,381 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3526 >>>>>>> ACTG content number of A's = 14,094,179 bp (23.94%) number of C's = 10,671,210 bp (18.13%) number of T's = 19,254,885 bp (32.71%) number of G's = 14,848,770 bp (25.22%) number of N's = 785 bp (0%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 312,257 number of insertions = 4,282 mapped reads with insertion percentage = 0.41% number of deletions = 11,709 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.42% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.1919X There is a 1.76% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4844457 0.01943608798471158 0.23915621302859416 chr2 243199373 5769359 0.02372275441680518 0.26545573725102933 chr3 198022430 4185211 0.02113503505638225 0.15975792920810367 chr4 191154276 3423052 0.017907274017767722 0.14785526601990343 chr5 180915260 3166909 0.017504930208761826 0.13944131684230113 chr6 171115067 3316460 0.019381461014184097 0.15999701337824854 chr7 159138663 2933068 0.01843089507419074 0.3219761548099463 chr8 146364022 4898080 0.033465054683998775 0.21830814512539676 chr9 141213431 2420907 0.017143603004731185 0.15471312142891128 chr10 135534747 2817575 0.02078858051064942 0.25302593383153804 chr11 135006516 1781802 0.013197896314871203 0.1402493100470285 chr12 133851895 2705689 0.020214050761104278 0.15772380785522977 chr13 115169878 1553977 0.01349291174902521 0.12296702736845809 chr14 107349540 1893263 0.017636433281409496 0.14293485130308387 chr15 102531392 1391704 0.013573442951013481 0.12573605655619127 chr16 90354753 1783740 0.019741518191079555 0.15640862858912993 chr17 81195210 2413685 0.029726938325549006 0.18879317979919674 chr18 78077248 1410652 0.018067388850590636 0.21788722572324257 chr19 59128983 1194709 0.02020513358059955 0.22829039289849212 chr20 63025520 1271410 0.020172939469598982 0.15443879023441678 chr21 48129895 605544 0.012581452754052341 0.12112759765407652 chr22 51304566 844534 0.016461185930312712 0.136267157513154 chrMT 16571 8411 0.507573471727717 0.7707384435941294 chrX 155270560 2117156 0.013635269944283063 0.1393573795660092 chrY 59373566 136856 0.002304998827255887 0.06888301611756983