BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094133.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 502,792 number of mapped reads = 470,693 (93.62%) number of supplementary alignments = 4,328 (0.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 235,954 number of mapped paired reads (second in pair) = 234,739 number of mapped paired reads (both in pair) = 468,038 number of mapped paired reads (singletons) = 2,655 number of mapped bases = 68,338,155 bp number of sequenced bases = 68,235,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 469,559 duplication rate = 38.78% >>>>>>> Insert size mean insert size = 17,424.0821 std insert size = 1,110,101.3338 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 23.9542 >>>>>>> ACTG content number of A's = 19,001,758 bp (27.85%) number of C's = 14,628,082 bp (21.44%) number of T's = 19,325,631 bp (28.32%) number of G's = 15,279,097 bp (22.39%) number of N's = 1,021 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0174 number of mismatches = 1,147,745 number of insertions = 25,552 mapped reads with insertion percentage = 5.35% number of deletions = 63,305 mapped reads with deletion percentage = 13.08% homopolymer indels = 62.54% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 36.4651X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 69724 2.797345086654769E-4 0.23880972102847436 chr2 243199373 1167278 0.004799675203110002 3.013017130049412 chr3 198022430 32288 1.6305223605224924E-4 0.09206773553026967 chr4 191154276 443679 0.0023210519235258957 1.6999902986698225 chr5 180915260 11193 6.186874451607897E-5 0.017723307936478156 chr6 171115067 115523 6.751188076266831E-4 0.32341481592209576 chr7 159138663 5218033 0.032789222314881454 28.556861226281452 chr8 146364022 13428 9.174385765376138E-5 0.03868859745097785 chr9 141213431 170634 0.0012083411527618786 0.8042457820693385 chr10 135534747 78188 5.768852765114174E-4 0.2477040092134832 chr11 135006516 15266 1.1307602367873859E-4 0.028720098371810217 chr12 133851895 12114 9.050301454454567E-5 0.019414329307389285 chr13 115169878 8169 7.093000480559683E-5 0.015471367290020596 chr14 107349540 6705 6.245951310084794E-5 0.0303295062711763 chr15 102531392 7411 7.228030221222393E-5 0.018411243874234973 chr16 90354753 124706 0.0013801819589944538 0.9737162339434369 chr17 81195210 42959 5.290829348184456E-4 0.3095352121228498 chr18 78077248 5865 7.511791399205053E-5 0.011522725861731765 chr19 59128983 4347 7.351724618703488E-5 0.010546375325276596 chr20 63025520 9729 1.543660409307214E-4 0.05343199803011327 chr21 48129895 1583 3.289016109426376E-5 0.008646095096143336 chr22 51304566 2117 4.1263383847745636E-5 0.008629895669210911 chrMT 16571 60592004 3656.5085993603284 15068.050262854915 chrX 155270560 178883 0.0011520728720241622 0.17076928197604965 chrY 59373566 6329 1.0659625867848328E-4 0.03553243664231087