BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777293.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,124,874 number of mapped reads = 1,092,167 (97.09%) number of supplementary alignments = 47,226 (4.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 548,820 number of mapped paired reads (second in pair) = 543,347 number of mapped paired reads (both in pair) = 1,083,692 number of mapped paired reads (singletons) = 8,475 number of mapped bases = 107,128,731 bp number of sequenced bases = 107,092,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,903 duplication rate = 4.56% >>>>>>> Insert size mean insert size = 207,683.705 std insert size = 4,334,817.5362 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 53.0272 >>>>>>> ACTG content number of A's = 31,086,535 bp (29.03%) number of C's = 22,547,336 bp (21.05%) number of T's = 30,528,068 bp (28.51%) number of G's = 22,929,315 bp (21.41%) number of N's = 1,656 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 630,171 number of insertions = 24,270 mapped reads with insertion percentage = 2.17% number of deletions = 13,796 mapped reads with deletion percentage = 1.22% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.4236X There is a 2.65% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.06% 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 9046558 0.036295026923924896 0.7849768522802342 chr2 243199373 9164208 0.0376818734643695 0.343392352587198 chr3 198022430 7140382 0.03605845055027352 0.24431807302543856 chr4 191154276 6973544 0.03648123466513509 0.412946590932935 chr5 180915260 6413322 0.03544931477864278 0.22725300636438206 chr6 171115067 6155737 0.035974254680915974 0.2939475200816317 chr7 159138663 5692530 0.03577087988982288 0.3376626231448476 chr8 146364022 5396355 0.03686940906830232 0.25809862876920153 chr9 141213431 4587216 0.032484275521922554 0.4102529943141237 chr10 135534747 5864307 0.043267923021983436 1.0054960474193593 chr11 135006516 5092204 0.03771820909740386 0.28528438323869737 chr12 133851895 4794495 0.03581940322921838 0.22603903812522685 chr13 115169878 3222274 0.027978444155337213 0.19979387549862831 chr14 107349540 3245912 0.030236850572438412 0.20998347272615825 chr15 102531392 3135527 0.030581141432274712 0.20888674806509064 chr16 90354753 3414632 0.037791393220896745 0.2882632479262929 chr17 81195210 3094270 0.03810902145582233 0.28475999406509533 chr18 78077248 2923775 0.03744720869260146 0.4915348651987661 chr19 59128983 2078627 0.035154113846334885 0.4743505033978059 chr20 63025520 2448008 0.038841535936553956 0.24881833846825832 chr21 48129895 1465869 0.030456517721470202 0.2690003950579535 chr22 51304566 1363159 0.026569935315308973 0.1962723219154309 chrMT 16571 469349 28.3235169875083 8.161476110095302 chrX 155270560 2918741 0.018797774671515322 0.1781866107378448 chrY 59373566 1027730 0.017309554895186856 0.39529114241355146