BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240194.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 = 2,519,363 number of mapped reads = 1,975,883 (78.43%) number of supplementary alignments = 9,472 (0.38%) number of secondary alignments = 0 number of mapped bases = 120,036,731 bp number of sequenced bases = 119,971,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,350 duplication rate = 8.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8898 >>>>>>> ACTG content number of A's = 31,883,920 bp (26.58%) number of C's = 20,777,023 bp (17.32%) number of T's = 39,370,582 bp (32.82%) number of G's = 27,912,808 bp (23.27%) number of N's = 26,996 bp (0.02%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,126,617 number of insertions = 8,347 mapped reads with insertion percentage = 0.42% number of deletions = 38,283 mapped reads with deletion percentage = 1.91% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3701X There is a 2.81% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% 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 8938912 0.035863148361022536 0.5325819515615685 chr2 243199373 12148589 0.04995320855535265 0.49391847932077354 chr3 198022430 8484979 0.042848575285133104 0.2730022427702916 chr4 191154276 7505243 0.03926275235402006 0.273635629001607 chr5 180915260 7432463 0.0410825653955338 0.27131084561053825 chr6 171115067 6634786 0.038773826971063866 0.32337507585609027 chr7 159138663 6537305 0.04107930076049464 0.5929705816915103 chr8 146364022 6646158 0.04540841327795706 0.4350314970455243 chr9 141213431 4765859 0.033749332243049886 0.3519527860571709 chr10 135534747 5678918 0.04190008928116419 0.31350924585305323 chr11 135006516 5594216 0.041436637028689785 0.3736799383181812 chr12 133851895 5837595 0.043612344823358684 0.2796511371956825 chr13 115169878 2834045 0.02460751933765181 0.2053136599269849 chr14 107349540 4130996 0.03848172987047732 0.27466923511438807 chr15 102531392 3057706 0.02982214461693839 0.260306377941618 chr16 90354753 3423041 0.037884459714034084 0.2639185742055003 chr17 81195210 2739310 0.03373733499796355 0.2689084820609218 chr18 78077248 3068059 0.039295173415948265 0.5514693961679312 chr19 59128983 2085854 0.03527633817074107 0.38842781293842027 chr20 63025520 2564682 0.04069275430016286 0.2695367861076968 chr21 48129895 1919466 0.039880951329729686 0.2756513768480343 chr22 51304566 1069311 0.02084241390912458 0.18469772833961168 chrMT 16571 36617 2.209703699233601 2.520305840073206 chrX 155270560 6639423 0.0427603468423119 0.3047783092301833 chrY 59373566 263198 0.004432915482960886 0.09232741455101023