BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084909.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 = 1,793,725 number of mapped reads = 1,622,523 (90.46%) number of supplementary alignments = 18,668 (1.04%) number of secondary alignments = 0 number of mapped bases = 108,590,550 bp number of sequenced bases = 108,548,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,875 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3797 >>>>>>> ACTG content number of A's = 29,605,013 bp (27.27%) number of C's = 20,497,036 bp (18.88%) number of T's = 33,883,086 bp (31.21%) number of G's = 24,548,426 bp (22.62%) number of N's = 15,314 bp (0.01%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 808,699 number of insertions = 8,534 mapped reads with insertion percentage = 0.52% number of deletions = 25,073 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.26X There is a 2.97% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% 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% 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 8340301 0.033461505397814034 0.33088915427264426 chr2 243199373 10235859 0.04208834452875008 0.40636229753102265 chr3 198022430 8057193 0.040688284655430194 0.23177067355345077 chr4 191154276 6416475 0.033566996952765 0.21226772711233588 chr5 180915260 6816840 0.03767974022755184 0.2263172851159436 chr6 171115067 5609374 0.032781297978862374 0.22243564209887287 chr7 159138663 7692266 0.04833687712960112 0.2744282924865335 chr8 146364022 6193586 0.04231631459266677 0.27032180241530895 chr9 141213431 7542410 0.0534114209008915 0.30723469798644265 chr10 135534747 5091216 0.03756391709647711 0.2309391197683711 chr11 135006516 4103787 0.030396955062524537 0.23564879294869534 chr12 133851895 3679199 0.027487089368439646 0.19238697037603883 chr13 115169878 3859094 0.033507841347196705 0.2122918523960257 chr14 107349540 2574950 0.023986595564359194 0.1788911148817015 chr15 102531392 2599404 0.02535227455021775 0.18865447934464827 chr16 90354753 2185802 0.02419133390802363 0.18290999958228055 chr17 81195210 3526560 0.04343310399714466 0.24646977314986904 chr18 78077248 2877487 0.036854359928259764 0.3889933540915357 chr19 59128983 2413257 0.04081343661872216 0.2841080218743718 chr20 63025520 1810000 0.028718525448104198 0.19756038393392333 chr21 48129895 1179877 0.024514431207464715 0.18272270985378714 chr22 51304566 1108378 0.021603886094660657 0.16825985728089576 chrMT 16571 19629 1.1845392553255687 1.2774159503162017 chrX 155270560 4444962 0.02862720402373766 0.20056944721539402 chrY 59373566 212644 0.0035814591294718594 0.0741865577172342