BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472690.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 23,589,248 number of mapped reads = 23,372,046 (99.08%) number of supplementary alignments = 152,130 (0.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,710,717 number of mapped paired reads (second in pair) = 11,661,329 number of mapped paired reads (both in pair) = 23,239,760 number of mapped paired reads (singletons) = 132,286 number of mapped bases = 2,301,676,745 bp number of sequenced bases = 2,301,448,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,178,989 duplication rate = 48.48% >>>>>>> Insert size mean insert size = 21,839.0908 std insert size = 1,492,935.3862 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 54.3758 >>>>>>> ACTG content number of A's = 619,316,341 bp (26.91%) number of C's = 532,427,642 bp (23.13%) number of T's = 618,563,741 bp (26.88%) number of G's = 530,682,679 bp (23.06%) number of N's = 457,915 bp (0.02%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 14,090,051 number of insertions = 136,652 mapped reads with insertion percentage = 0.58% number of deletions = 108,318 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.7435X std coverageData = 71.2529X There is a 3.78% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 322632529 1.29441013107847 107.80568122817918 chr2 243199373 152231257 0.6259525060535415 37.8228465820279 chr3 198022430 198893428 1.0043984815255524 32.94952123644547 chr4 191154276 55353601 0.28957553112753803 15.334733207831022 chr5 180915260 137716538 0.7612212369481712 147.23092154977604 chr6 171115067 84004844 0.49092605036352527 19.300794285063695 chr7 159138663 167495691 1.0525141272551723 147.44437177645264 chr8 146364022 89301649 0.6101338824919692 24.886705291781276 chr9 141213431 90626957 0.6417729273924376 33.87846502956303 chr10 135534747 34057527 0.2512826249640618 13.842304615721972 chr11 135006516 84042495 0.6225069536643698 26.985760930613516 chr12 133851895 62678615 0.4682684171187864 21.41401900221658 chr13 115169878 75009107 0.6512910172571339 45.27372547212844 chr14 107349540 43300823 0.4033629114759132 18.28631958336527 chr15 102531392 67469227 0.6580348289819375 47.06088277806858 chr16 90354753 187567552 2.0759013308353573 164.98512198605727 chr17 81195210 157279099 1.9370489835545717 88.9978034004169 chr18 78077248 23268842 0.2980233370930287 21.0195742517368 chr19 59128983 56715878 0.9591891340326283 37.72759929453839 chr20 63025520 63918997 1.0141764320230915 51.056238864708796 chr21 48129895 15636805 0.32488757766872334 33.032028183718865 chr22 51304566 18210446 0.3549478617556184 12.284780645057896 chrMT 16571 12433 0.7502866453442761 1.1223151170325993 chrX 155270560 113837089 0.733153078085118 49.67939200145688 chrY 59373566 415316 0.006994964728916569 0.5694191255211539