BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708559.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,454,817 number of mapped reads = 3,651,973 (81.98%) number of supplementary alignments = 83 (0%) number of secondary alignments = 0 number of mapped bases = 182,119,030 bp number of sequenced bases = 182,102,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,548 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3439 >>>>>>> ACTG content number of A's = 56,506,622 bp (31.03%) number of C's = 34,458,615 bp (18.92%) number of T's = 56,387,656 bp (30.96%) number of G's = 34,742,492 bp (19.08%) number of N's = 7,517 bp (0%) GC percentage = 38% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 288,041 number of insertions = 12,387 mapped reads with insertion percentage = 0.34% number of deletions = 9,632 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0588X std coverageData = 0.2511X There is a 5.53% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.02% 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 13691398 0.054930246292144644 0.24375945870258076 chr2 243199373 15034281 0.0618187490146202 0.2562311105719624 chr3 198022430 14774792 0.07461170939069882 0.28220885640927834 chr4 191154276 16975788 0.08880673953639415 0.3072014933230845 chr5 180915260 12556910 0.06940768843932789 0.27136683213897184 chr6 171115067 11783143 0.06886093204171202 0.27082122006516857 chr7 159138663 10262483 0.06448767889925028 0.2624558052578777 chr8 146364022 10901447 0.07448173978165208 0.28151842868514265 chr9 141213431 7381300 0.052270523757757856 0.23656259753243963 chr10 135534747 8062726 0.0594882580184401 0.2515592364831914 chr11 135006516 7987644 0.05916487764190582 0.2520733368122712 chr12 133851895 8238174 0.06154693588760921 0.25698956910609555 chr13 115169878 7388716 0.06415493467831927 0.2624215430891043 chr14 107349540 5148006 0.04795554783001399 0.22677224435997093 chr15 102531392 3945423 0.038480146646209586 0.20346480752460716 chr16 90354753 3370344 0.03730123638321495 0.19902781126813962 chr17 81195210 2639486 0.032507902867669164 0.1857265972838648 chr18 78077248 5136110 0.06578241589662587 0.2637353573041547 chr19 59128983 1434800 0.0242655957739033 0.1598780960124816 chr20 63025520 2798536 0.04440321952123521 0.21754441003601965 chr21 48129895 1993064 0.041410104883877266 0.21093621949802135 chr22 51304566 952558 0.018566729518772265 0.14051920348995225 chrMT 16571 50 0.003017319413433106 0.05484719862481972 chrX 155270560 9434119 0.06075922570254142 0.254782329489258 chrY 59373566 227732 0.0038355789510773194 0.0648077637872624