BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472828.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 = 2,833,343 number of mapped reads = 2,351,561 (83%) number of supplementary alignments = 16,221 (0.57%) number of secondary alignments = 0 number of mapped bases = 152,528,406 bp number of sequenced bases = 152,465,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,570 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7189 >>>>>>> ACTG content number of A's = 41,499,616 bp (27.22%) number of C's = 29,350,272 bp (19.25%) number of T's = 46,390,294 bp (30.43%) number of G's = 35,221,788 bp (23.1%) number of N's = 3,639 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,312,473 number of insertions = 12,214 mapped reads with insertion percentage = 0.51% number of deletions = 35,575 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.3504X There is a 4.27% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11160219 0.04477509004882279 0.4295902942013261 chr2 243199373 14825692 0.060961061770500535 0.5147437166130133 chr3 198022430 11747649 0.059324840120384345 0.27171421644804356 chr4 191154276 8373559 0.04380524032849781 0.25495794377299663 chr5 180915260 7821699 0.04323404780779687 0.2332497493476313 chr6 171115067 9417391 0.055035428294575604 0.2886150127195695 chr7 159138663 9270829 0.05825629564325295 0.4574796591735017 chr8 146364022 8286491 0.0566156278487619 0.3698866929747455 chr9 141213431 8908774 0.06308729939434728 0.43202969967067534 chr10 135534747 6179730 0.045595171251546295 0.29752296690421676 chr11 135006516 5053356 0.03743046002312955 0.33874880371746297 chr12 133851895 6381254 0.04767399071936934 0.25140687733967587 chr13 115169878 6190428 0.053750408592079954 0.26784855342976105 chr14 107349540 3118208 0.029047241376162394 0.23442889000897102 chr15 102531392 2856268 0.027857497535974152 0.20310115773714374 chr16 90354753 4964645 0.0549461410181709 0.2905617631838039 chr17 81195210 3221748 0.039679040179833265 0.24361937588510305 chr18 78077248 2560549 0.032795072387797275 0.656829365915763 chr19 59128983 3362531 0.05686772931643353 0.35672855683691096 chr20 63025520 6383854 0.10128998539004518 0.38354045053725594 chr21 48129895 2226596 0.04626222434102547 0.2781323714581494 chr22 51304566 1728337 0.033687781317553685 0.21724349504752438 chrMT 16571 85441 5.156055760062761 4.547451453553262 chrX 155270560 7656381 0.049309933576590435 0.2835986416845634 chrY 59373566 746777 0.01257760061101939 0.16185376244701252