BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472809.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,663,090 number of mapped reads = 2,083,708 (78.24%) number of supplementary alignments = 20,988 (0.79%) number of secondary alignments = 0 number of mapped bases = 131,938,872 bp number of sequenced bases = 131,882,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,912 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4557 >>>>>>> ACTG content number of A's = 34,890,402 bp (26.46%) number of C's = 27,067,516 bp (20.52%) number of T's = 38,492,897 bp (29.19%) number of G's = 31,428,672 bp (23.83%) number of N's = 2,553 bp (0%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,165,506 number of insertions = 10,762 mapped reads with insertion percentage = 0.51% number of deletions = 31,283 mapped reads with deletion percentage = 1.48% homopolymer indels = 43.76% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.3414X There is a 3.57% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 10743022 0.043101284790780924 0.45289590160396814 chr2 243199373 11173986 0.045945784572396904 0.473917025302273 chr3 198022430 9493069 0.04793936222275426 0.25602246315893207 chr4 191154276 5973351 0.03124884844323336 0.24348130376725324 chr5 180915260 7286224 0.040274236678542207 0.23621148956685512 chr6 171115067 8684918 0.05075484089311668 0.2894249632905428 chr7 159138663 7145171 0.04489902620333061 0.4183262718796722 chr8 146364022 6632313 0.04531382035948698 0.3132093191907123 chr9 141213431 6220502 0.04405035665481423 0.3616393619232584 chr10 135534747 6234258 0.04599748874729519 0.3632977777274354 chr11 135006516 4948633 0.03665477153710121 0.34769069539772013 chr12 133851895 6117770 0.04570551653377788 0.25466011516182235 chr13 115169878 7527955 0.0653639226742951 0.3032957053481557 chr14 107349540 3203388 0.029840724049679208 0.2398795433454029 chr15 102531392 3031623 0.029567754234722573 0.22635150601125584 chr16 90354753 4078964 0.04514387859596052 0.28418671774143667 chr17 81195210 3430731 0.04225287427669686 0.2607749765324769 chr18 78077248 2759750 0.03534640462737621 0.6529915890347594 chr19 59128983 3212052 0.0543228013916627 0.37908792689162385 chr20 63025520 4186428 0.06642433096942318 0.3202548844999878 chr21 48129895 1775146 0.036882399182462375 0.2651537789006333 chr22 51304566 1794191 0.03497137077428937 0.2272818968156276 chrMT 16571 102056 6.158711001146582 4.702797857338488 chrX 155270560 5516641 0.035529214295356444 0.2613274030369957 chrY 59373566 666730 0.011229408050040315 0.1731659735727458