BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008669.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 = 1,754,149 number of mapped reads = 677,363 (38.61%) number of supplementary alignments = 8,408 (0.48%) number of secondary alignments = 0 number of mapped bases = 44,355,126 bp number of sequenced bases = 44,335,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,076 duplication rate = 6.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4423 >>>>>>> ACTG content number of A's = 12,108,784 bp (27.31%) number of C's = 8,392,754 bp (18.93%) number of T's = 13,806,310 bp (31.14%) number of G's = 9,964,316 bp (22.47%) number of N's = 63,207 bp (0.14%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 368,236 number of insertions = 3,130 mapped reads with insertion percentage = 0.46% number of deletions = 10,986 mapped reads with deletion percentage = 1.61% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.207X There is a 0.93% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 3179727 0.012757147754508502 0.30722757766212516 chr2 243199373 3041428 0.012505903952309943 0.22133765644785114 chr3 198022430 2675288 0.013510025101701862 0.1673100757014408 chr4 191154276 2764813 0.014463777938192708 0.18427260766340167 chr5 180915260 2796468 0.015457336213650523 0.18090220363363332 chr6 171115067 2457212 0.014359997883763211 0.18651709674217778 chr7 159138663 2242259 0.014089970078484322 0.19368551395762734 chr8 146364022 2545970 0.017394780255492022 0.2605113292554867 chr9 141213431 1811898 0.012830918328158176 0.17995150798817364 chr10 135534747 1773275 0.013083545284516596 0.19020487561301067 chr11 135006516 1959835 0.014516595628613954 0.19177892189449966 chr12 133851895 1654156 0.012358106696957858 0.1645504594538874 chr13 115169878 2302144 0.019989115556760424 0.21229824432268807 chr14 107349540 1487545 0.013857022582490806 0.1840752813950696 chr15 102531392 1293427 0.012614936506470135 0.16868255325828221 chr16 90354753 1486190 0.01644838761276897 0.20080119169829766 chr17 81195210 1149709 0.014159813121980964 0.1740860340737243 chr18 78077248 1416814 0.01814631068963906 0.2694140886355232 chr19 59128983 1034383 0.017493671419987047 0.24645214996207584 chr20 63025520 900764 0.014292051854550347 0.17558215169102417 chr21 48129895 598790 0.012441124170331143 0.19046580992395265 chr22 51304566 608972 0.01186974274375501 0.1569409433298553 chrMT 16571 23256 1.4034156055760063 1.8381451550851278 chrX 155270560 3020998 0.019456347681105806 0.21097957740254836 chrY 59373566 129805 0.0021862422748871106 0.07112733473261261