BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549152.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,547,033 number of mapped reads = 11,899,771 (87.84%) number of secondary alignments = 0 number of mapped bases = 471,959,886 bp number of sequenced bases = 471,911,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 714,532 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3747 >>>>>>> ACTG content number of A's = 133,058,648 bp (28.2%) number of C's = 101,673,772 bp (21.55%) number of T's = 135,014,009 bp (28.61%) number of G's = 102,069,288 bp (21.63%) number of N's = 96,269 bp (0.02%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,502,384 number of insertions = 12,896 mapped reads with insertion percentage = 0.11% number of deletions = 37,853 mapped reads with deletion percentage = 0.32% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.1525X std coverageData = 0.8892X There is a 10.44% of reference with a coverageData >= 1X There is a 3% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 39480283 0.15839592632348948 1.5432783871166749 chr2 243199373 39577673 0.16273756182751342 0.8621805439318514 chr3 198022430 31493052 0.15903780192981168 0.5511885956871072 chr4 191154276 28337378 0.14824349521744415 0.5592462394318469 chr5 180915260 28501813 0.15754233777736604 0.5666004708056477 chr6 171115067 26859247 0.15696599645430406 0.6376019480174921 chr7 159138663 26915226 0.1691306530582075 1.4626253510956686 chr8 146364022 23732648 0.16214809948308198 0.8450344332144659 chr9 141213431 20317277 0.14387637816122462 0.8498719321068164 chr10 135534747 22741918 0.1677940048834857 0.8087793717584485 chr11 135006516 22000150 0.16295620872106648 0.7768654000385044 chr12 133851895 21810457 0.16294470093232524 0.5944673427419449 chr13 115169878 14094522 0.12238028071888728 0.47511766227410435 chr14 107349540 14662813 0.1365894348499304 0.7217818792148073 chr15 102531392 14670537 0.14308336904272206 0.5161192306191426 chr16 90354753 15345130 0.16983201758074642 0.6336924046040578 chr17 81195210 14925432 0.18382158257857822 0.6532185457594207 chr18 78077248 12204868 0.15631785587524807 1.73943107954873 chr19 59128983 11680479 0.19754236260075705 1.4235313826418288 chr20 63025520 11007302 0.1746483329292642 0.624235772462547 chr21 48129895 6304776 0.13099500840382053 0.6063089193297769 chr22 51304566 6671248 0.13003224703235966 0.5423773645364613 chrMT 16571 167018 10.07893307585541 13.6675857506307 chrX 155270560 14991029 0.09654778729464233 0.5678552488508323 chrY 59373566 3467610 0.0584032631626 0.4392782808812647