BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717074.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 = 1,161,005 number of mapped reads = 972,108 (83.73%) number of supplementary alignments = 4,234 (0.36%) number of secondary alignments = 0 number of mapped bases = 54,445,536 bp number of sequenced bases = 54,429,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,085 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6377 >>>>>>> ACTG content number of A's = 13,636,198 bp (25.05%) number of C's = 10,372,208 bp (19.06%) number of T's = 17,250,953 bp (31.69%) number of G's = 13,169,322 bp (24.2%) number of N's = 924 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 285,854 number of insertions = 3,994 mapped reads with insertion percentage = 0.41% number of deletions = 10,022 mapped reads with deletion percentage = 1.02% homopolymer indels = 40.72% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 0.1824X There is a 1.63% of reference with a coverageData >= 1X There is a 0.09% 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 4644261 0.018632896405100633 0.22069717308979891 chr2 243199373 5325426 0.021897367309413253 0.25102522254430415 chr3 198022430 4102674 0.020718228738027304 0.1563920356807958 chr4 191154276 3036339 0.01588423269171337 0.1371857463029241 chr5 180915260 2928006 0.01618440589257092 0.13435158093560243 chr6 171115067 3029969 0.017707201669155178 0.14990324005773126 chr7 159138663 2692148 0.01691699521190523 0.3357906693406555 chr8 146364022 3790421 0.025897218101863857 0.18787604014170156 chr9 141213431 2323728 0.016455431919928352 0.14913049755691907 chr10 135534747 2812089 0.02074810380543965 0.21934779031432217 chr11 135006516 1864331 0.013809192735556556 0.14311325154936455 chr12 133851895 2433300 0.018179047819980435 0.14585697482188367 chr13 115169878 1378675 0.011970795002491885 0.11438936583132182 chr14 107349540 1742076 0.016228071401144337 0.1369056244764208 chr15 102531392 1305488 0.012732568772693537 0.1230869659295056 chr16 90354753 1714741 0.01897787269696814 0.15200092377256716 chr17 81195210 2051744 0.02526927388943264 0.17321810223288153 chr18 78077248 1301326 0.01666716019499048 0.20372989951213225 chr19 59128983 1198953 0.020276908872253054 0.21433255937433002 chr20 63025520 1239541 0.01966728715605996 0.1498141483724205 chr21 48129895 564196 0.011722360915185874 0.1158059488386507 chr22 51304566 889291 0.017333564423876034 0.1406476350809808 chrMT 16571 19426 1.1722889385070303 1.3936227930177347 chrX 155270560 1924571 0.01239495110985624 0.12856726557660778 chrY 59373566 132816 0.002236955078628762 0.06420533619765517