BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,170,900 number of mapped reads = 11,900,970 (97.78%) number of supplementary alignments = 84,736 (0.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,966,033 number of mapped paired reads (second in pair) = 5,934,937 number of mapped paired reads (both in pair) = 11,807,722 number of mapped paired reads (singletons) = 93,248 number of mapped bases = 1,132,471,694 bp number of sequenced bases = 1,131,582,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 511,481 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 74,182.4172 std insert size = 2,648,629.608 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.7135 >>>>>>> ACTG content number of A's = 325,373,544 bp (28.75%) number of C's = 226,572,680 bp (20.02%) number of T's = 328,849,055 bp (29.06%) number of G's = 250,536,523 bp (22.14%) number of N's = 250,257 bp (0.02%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 10,626,829 number of insertions = 187,000 mapped reads with insertion percentage = 1.54% number of deletions = 623,476 mapped reads with deletion percentage = 5.1% homopolymer indels = 53.02% >>>>>>> Coverage mean coverageData = 0.3658X std coverageData = 1.7423X There is a 20.35% of reference with a coverageData >= 1X There is a 8.45% of reference with a coverageData >= 2X There is a 3.62% of reference with a coverageData >= 3X There is a 1.7% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 90545634 0.3632714479776562 2.4165242800998326 chr2 243199373 98689446 0.40579646560190763 2.722657239784354 chr3 198022430 74681300 0.3771355598454175 0.9311672835295498 chr4 191154276 68701091 0.3594012775314532 1.5899374513026425 chr5 180915260 70292817 0.38854001038939445 0.9361251012412579 chr6 171115067 64017454 0.37411932872048026 1.5416802668285559 chr7 159138663 55328223 0.3476730415914076 1.2398101731027769 chr8 146364022 58978155 0.40295527680976134 1.108982552448736 chr9 141213431 50083257 0.354663551797704 2.046311550624959 chr10 135534747 59739283 0.4407672889963782 3.587612619548429 chr11 135006516 55507549 0.4111471849255039 1.2198952723536611 chr12 133851895 49827399 0.3722577031875417 0.9339042820932414 chr13 115169878 33317304 0.289288350205598 0.7964937389722416 chr14 107349540 33541124 0.3124477664273177 0.8622779761491839 chr15 102531392 34048360 0.3320774187870189 0.8895711150404462 chr16 90354753 34396451 0.38068225364967795 2.189246731071406 chr17 81195210 29614357 0.3647303455462459 1.2703692788589485 chr18 78077248 31167209 0.39918426684301167 2.2445383909540912 chr19 59128983 16650368 0.2815940196366983 1.416907323698525 chr20 63025520 27609987 0.4380763062327768 1.099707014730529 chr21 48129895 14829125 0.3081063235230411 1.3365523138623963 chr22 51304566 14171547 0.2762238939902542 0.8534374974112446 chrMT 16571 283017 17.079053768631947 13.515818964978559 chrX 155270560 64327691 0.41429419073390344 1.0654092783939537 chrY 59373566 2123546 0.035765849064885204 1.5117472051918153