BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238633.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,623,610 number of mapped reads = 1,466,808 (90.34%) number of supplementary alignments = 11,989 (0.74%) number of secondary alignments = 0 number of mapped bases = 89,641,362 bp number of sequenced bases = 89,597,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,909 duplication rate = 15.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.422 >>>>>>> ACTG content number of A's = 21,656,301 bp (24.17%) number of C's = 15,455,432 bp (17.25%) number of T's = 30,552,160 bp (34.1%) number of G's = 21,928,811 bp (24.47%) number of N's = 4,366 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 532,758 number of insertions = 5,711 mapped reads with insertion percentage = 0.39% number of deletions = 26,139 mapped reads with deletion percentage = 1.77% homopolymer indels = 42.14% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.3973X There is a 1.92% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 9907607 0.039749577996036366 0.489434538273582 chr2 243199373 5354604 0.022017342947672814 0.8741025958207975 chr3 198022430 5222303 0.026372280150283985 0.23437501763787846 chr4 191154276 2480628 0.012977099188720215 0.1637158501753627 chr5 180915260 4185794 0.0231367657985291 0.2201579392838975 chr6 171115067 5298184 0.030962697165644683 0.38349067739725073 chr7 159138663 7621801 0.04789408718357776 0.47790720552390137 chr8 146364022 5531427 0.03779225881070691 0.34412782402571956 chr9 141213431 3504327 0.024815819396102626 0.2614572627963737 chr10 135534747 4884088 0.03603568906208236 0.290192025084052 chr11 135006516 5367854 0.03975996240062961 0.31564067253627076 chr12 133851895 3366728 0.02515263605345296 0.23045783271716958 chr13 115169878 2374554 0.02061783898043202 0.26899116555588165 chr14 107349540 2930509 0.027298756939247246 0.24254140376811797 chr15 102531392 1259131 0.012280443827388982 0.24466714201771209 chr16 90354753 1970399 0.021807364135011248 0.22485741337056156 chr17 81195210 1923486 0.023689648687404096 0.22464838942710785 chr18 78077248 3703596 0.04743502229996631 0.6751471914425 chr19 59128983 2410340 0.04076410378984533 0.4043406015918942 chr20 63025520 1893753 0.030047399846919152 0.25348674776456187 chr21 48129895 1997284 0.0414977842773187 0.30043792088189825 chr22 51304566 1355854 0.026427550327586827 0.23507137309972373 chrMT 16571 16184 0.9766459477400278 1.4607886646055983 chrX 155270560 4868688 0.031356156633942714 0.25576420412545225 chrY 59373566 212239 0.003574637912097111 0.15385516498026597