BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514719.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 70,631,827 number of mapped reads = 66,212,298 (93.74%) number of supplementary alignments = 4,003,821 (5.67%) number of secondary alignments = 0 number of mapped bases = 6,035,275,719 bp number of sequenced bases = 6,026,551,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,919,607 duplication rate = 41.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2581 >>>>>>> ACTG content number of A's = 1,611,440,747 bp (26.74%) number of C's = 1,348,424,753 bp (22.37%) number of T's = 1,630,584,371 bp (27.06%) number of G's = 1,361,816,968 bp (22.6%) number of N's = 74,284,985 bp (1.23%) GC percentage = 44.97% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 64,706,145 number of insertions = 3,278,034 mapped reads with insertion percentage = 4.55% number of deletions = 2,992,008 mapped reads with deletion percentage = 4.03% homopolymer indels = 29.61% >>>>>>> Coverage mean coverageData = 1.9496X std coverageData = 282.3012X There is a 6.52% of reference with a coverageData >= 1X There is a 3.37% of reference with a coverageData >= 2X There is a 2.18% of reference with a coverageData >= 3X There is a 1.66% of reference with a coverageData >= 4X There is a 1.36% of reference with a coverageData >= 5X There is a 1.17% of reference with a coverageData >= 6X There is a 1.03% of reference with a coverageData >= 7X There is a 0.94% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.8% of reference with a coverageData >= 10X There is a 0.75% of reference with a coverageData >= 11X There is a 0.71% of reference with a coverageData >= 12X There is a 0.67% of reference with a coverageData >= 13X There is a 0.64% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.59% of reference with a coverageData >= 16X There is a 0.57% of reference with a coverageData >= 17X There is a 0.55% of reference with a coverageData >= 18X There is a 0.54% of reference with a coverageData >= 19X There is a 0.52% of reference with a coverageData >= 20X There is a 0.51% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.48% of reference with a coverageData >= 23X There is a 0.47% of reference with a coverageData >= 24X There is a 0.46% of reference with a coverageData >= 25X There is a 0.45% of reference with a coverageData >= 26X There is a 0.44% of reference with a coverageData >= 27X There is a 0.43% of reference with a coverageData >= 28X There is a 0.42% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.41% of reference with a coverageData >= 31X There is a 0.4% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.39% of reference with a coverageData >= 34X There is a 0.38% of reference with a coverageData >= 35X There is a 0.37% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.36% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.35% of reference with a coverageData >= 41X There is a 0.34% of reference with a coverageData >= 42X There is a 0.34% of reference with a coverageData >= 43X There is a 0.33% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.32% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.31% of reference with a coverageData >= 49X There is a 0.31% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 518255816 2.0792558667286127 81.04792388715833 chr2 243199373 360893497 1.4839409022654018 97.0084558737581 chr3 198022430 367084751 1.8537533904618786 74.48074605552331 chr4 191154276 452956432 2.3695856638854367 266.5932655272737 chr5 180915260 270544516 1.4954212043804376 71.7704150329935 chr6 171115067 320933495 1.8755420000507612 83.34656682964699 chr7 159138663 237544869 1.492691119316492 48.54488139851567 chr8 146364022 304808905 2.0825398266248794 209.85908623579016 chr9 141213431 205085959 1.4523119900684234 95.25814810206776 chr10 135534747 380966268 2.8108383749002757 227.38128312113037 chr11 135006516 240526079 1.781588667912888 52.96157771955181 chr12 133851895 257501466 1.9237790096285152 74.06862884398988 chr13 115169878 123806779 1.074992707728665 69.38884210763527 chr14 107349540 122927468 1.1451140638329702 50.50815853498631 chr15 102531392 206321568 2.0122770594980315 71.56830388694834 chr16 90354753 673551435 7.45452134654167 1497.1083162021032 chr17 81195210 181182176 2.231439219136203 74.60666197616509 chr18 78077248 214197859 2.7434094372793467 103.33451672544278 chr19 59128983 144346544 2.4412147254418364 86.94444837810926 chr20 63025520 92084496 1.4610668186474305 80.74532578932458 chr21 48129895 69024405 1.4341274793971606 50.38598799387429 chr22 51304566 69667362 1.3579173830259084 58.93021608993128 chrMT 16571 1364992 82.37233721561765 78.48480315154262 chrX 155270560 171192747 1.1025447902036292 63.105490421153625 chrY 59373566 48505835 0.8169601098239577 217.9310591021016