BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085090.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,015,716 number of mapped reads = 2,616,995 (86.78%) number of supplementary alignments = 21,610 (0.72%) number of secondary alignments = 0 number of mapped bases = 156,818,465 bp number of sequenced bases = 156,769,634 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,453 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6043 >>>>>>> ACTG content number of A's = 47,094,839 bp (30.04%) number of C's = 30,865,620 bp (19.69%) number of T's = 46,104,760 bp (29.41%) number of G's = 32,701,018 bp (20.86%) number of N's = 3,397 bp (0%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,297,677 number of insertions = 11,384 mapped reads with insertion percentage = 0.43% number of deletions = 31,042 mapped reads with deletion percentage = 1.17% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.4154X There is a 4.26% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.1% 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 12626391 0.05065741039818713 0.6857066096217158 chr2 243199373 12849291 0.052834391970245746 0.3729094850031335 chr3 198022430 11510268 0.05812608197970301 0.2764366834329381 chr4 191154276 11887791 0.06218951126157387 0.29283281481776774 chr5 180915260 9290729 0.051354037243734996 0.26148709898447203 chr6 171115067 10235264 0.05981509506699372 0.4062332175619598 chr7 159138663 8206303 0.051566997267031206 0.3582695416916645 chr8 146364022 7580860 0.05179455918477015 0.8838970166947353 chr9 141213431 6255179 0.04429592111532224 0.3459160031086486 chr10 135534747 7007332 0.051701369243711354 0.36331688924250877 chr11 135006516 6900093 0.0511093331228546 0.34178189275322074 chr12 133851895 7333183 0.054785798886149505 0.2756654016852861 chr13 115169878 4993124 0.043354426406529666 0.2381100792204019 chr14 107349540 5442658 0.05070033835263756 0.2743243602537808 chr15 102531392 4643954 0.04529299670485309 0.2442103097540305 chr16 90354753 3825381 0.04233735219219735 0.2535078960641007 chr17 81195210 3736165 0.046014598644427425 0.2746473426584248 chr18 78077248 4325898 0.055405359574148924 0.682722718637151 chr19 59128983 2362295 0.03995155810476226 0.4646901935910362 chr20 63025520 2877906 0.04566255066201755 0.2541942931485458 chr21 48129895 2041350 0.04241334829423584 0.24839531478990629 chr22 51304566 1453155 0.028324087177737746 0.18998285151419284 chrMT 16571 355808 21.471727717096133 11.753631292972447 chrX 155270560 8698007 0.05601839138082583 0.29955926872001987 chrY 59373566 380080 0.006401501974801379 0.11691281417012869