BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617358.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,101,589 (94.07%) number of supplementary alignments = 65,858 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,131,234 number of mapped paired reads (second in pair) = 14,970,355 number of mapped paired reads (both in pair) = 29,605,852 number of mapped paired reads (singletons) = 495,737 number of mapped bases = 2,956,856,085 bp number of sequenced bases = 2,955,986,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,551,738 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 51,559.2631 std insert size = 2,164,816.3428 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.4677 >>>>>>> ACTG content number of A's = 895,808,290 bp (30.3%) number of C's = 587,103,032 bp (19.86%) number of T's = 883,302,317 bp (29.88%) number of G's = 589,019,870 bp (19.93%) number of N's = 752,857 bp (0.03%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 33,054,858 number of insertions = 296,368 mapped reads with insertion percentage = 0.95% number of deletions = 361,563 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.9552X std coverageData = 9.7527X There is a 52.92% of reference with a coverageData >= 1X There is a 23.9% of reference with a coverageData >= 2X There is a 9.19% of reference with a coverageData >= 3X There is a 3.23% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191772241 0.769395238537841 19.813623470970953 chr2 243199373 292595673 1.203110309827978 8.780162257718262 chr3 198022430 235257666 1.1880354462875746 1.4649793238800317 chr4 191154276 162090609 0.8479570135276493 9.292395229527719 chr5 180915260 185696325 1.0264270963101731 1.4608750427408297 chr6 171115067 138840082 0.8113843183663073 3.690124851043689 chr7 159138663 239640581 1.505860213240575 10.819391059515713 chr8 146364022 124742565 0.8522761488475631 7.666173556008597 chr9 141213431 124634798 0.8825987522390841 14.83512557100252 chr10 135534747 124438334 0.918128647851462 20.236993681949148 chr11 135006516 158665789 1.1752454155620162 5.495950035440966 chr12 133851895 130514747 0.9750683544674508 1.3671175582876054 chr13 115169878 128839772 1.118693309721141 1.2907685304394831 chr14 107349540 85590057 0.797302503578497 1.3594227554983311 chr15 102531392 66497481 0.6485572828270975 0.9750923109846119 chr16 90354753 74233395 0.821577089585979 7.928196719388699 chr17 81195210 91866840 1.1314317679577404 7.072295273801669 chr18 78077248 53476348 0.6849158925273595 15.114599310876688 chr19 59128983 54516982 0.9220010092174256 9.4476449791746 chr20 63025520 84675447 1.343510485911104 2.457299122859036 chr21 48129895 46979083 0.9760894554205863 3.150560131996041 chr22 51304566 26105498 0.5088338141287464 0.9122787201889743 chrMT 16571 1968321 118.7810633033613 20.918641077254577 chrX 155270560 123117194 0.7929203965001479 2.9755186662427198 chrY 59373566 10100257 0.1701137000934052 8.226815283729625