BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708598.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 = 5,258,436 number of mapped reads = 5,042,790 (95.9%) number of supplementary alignments = 122 (0%) number of secondary alignments = 0 number of mapped bases = 251,551,520 bp number of sequenced bases = 251,530,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,955 duplication rate = 0.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.752 >>>>>>> ACTG content number of A's = 77,889,947 bp (30.97%) number of C's = 47,803,060 bp (19%) number of T's = 77,386,561 bp (30.77%) number of G's = 48,443,905 bp (19.26%) number of N's = 6,681 bp (0%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 357,188 number of insertions = 15,745 mapped reads with insertion percentage = 0.31% number of deletions = 12,583 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.56% >>>>>>> Coverage mean coverageData = 0.0813X std coverageData = 0.2972X There is a 7.5% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.04% 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 19133330 0.07676341957840097 0.2905558812764121 chr2 243199373 22070184 0.09074934580526242 0.31243082692742236 chr3 198022430 18819157 0.09503548158660613 0.3194871698670462 chr4 191154276 18341214 0.09594979711570774 0.32041396197796074 chr5 180915260 17934169 0.09913021709721999 0.32644918673952494 chr6 171115067 17324900 0.10124707487038531 0.3300234641457806 chr7 159138663 13226655 0.08311402616220295 0.2999327764034726 chr8 146364022 14472361 0.09887922456790645 0.3262831913194684 chr9 141213431 10478567 0.07420375615687717 0.28491371693779133 chr10 135534747 10631749 0.07844297669290666 0.29029420399397216 chr11 135006516 11310613 0.08377827482045386 0.3037739860046945 chr12 133851895 11905305 0.08894386590492424 0.31046378868461233 chr13 115169878 9722451 0.0844183493881968 0.30304451722255465 chr14 107349540 7958335 0.07413478436889435 0.28532012138307783 chr15 102531392 6847507 0.06678449269468613 0.2704358274108887 chr16 90354753 4608738 0.05100714513601736 0.23463736173057914 chr17 81195210 4287823 0.05280881717037249 0.2392620713248767 chr18 78077248 7197310 0.09218191194443738 0.3145385083542599 chr19 59128983 2136799 0.03613792917764204 0.1967340335125821 chr20 63025520 3784953 0.060054292293026695 0.25548611235015484 chr21 48129895 3079933 0.0639920988815787 0.2656001209384235 chr22 51304566 1507583 0.02938496741206231 0.17846544172313847 chrMT 16571 399 0.024078208919196185 0.1532920375441586 chrX 155270560 14411165 0.09281324804908284 0.316445539954228 chrY 59373566 360320 0.006068693936961779 0.08206142839402114