Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A13 F55 I0 R1	26	48.4	1146576	93.4%	1070901	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	100%	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,513,930	0	A	T	99.4%	92.0 / ‑6.7	34	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (1/0); major base T (15/17); minor base G (1/0); total (17/17)
Fisher's exact test for biased strand distribution p-value = 4.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513795‑1514062

tatatttGTATATATCCACTAATTAGTTGCCATTGGAATGAGGTTTCTCTCTGAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTg                                                                                                                                  <  2:138962/138‑1 (MQ=255)

        tatttatCGCTTTAGTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGa                                                                                                                          <  2:455213/140‑1 (MQ=255)

           gtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatta                                                                                                                       >  1:331071/1‑140 (MQ=255)

            tatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTCGTATGattat                                                                                                                      >  2:260290/1‑140 (MQ=255)

             atCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattatt                                                                                                                     >  1:90457/1‑140 (MQ=255)

                                   gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                               >  2:192244/1‑140 (MQ=255)

                                       ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                           <  2:1704/140‑1 (MQ=255)

                                               tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                   <  1:335322/140‑1 (MQ=255)

                                               tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                   <  1:515792/140‑1 (MQ=255)

                                               tagcgtGGAGAACGCGTACAAAAAATACTGGAATAAAAGTACCACAGCGCGTAAAAAAACCAGCATCTATATCACGTATAAGATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                   <  1:210426/135‑1 (MQ=255)

                                                  ctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATATATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAttt                                                                                <  2:495822/140‑1 (MQ=255)

                                                   ttGCATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                               <  1:236770/140‑1 (MQ=255)

                                                      gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATaa                                                                            <  1:1210/140‑1 (MQ=255)

                                                        tAAAGCGTACAACAAATACTGCAATAATAGTACCACATCGCGTTAAAAAACAAGCATCTATCTAACAGCTAAAATGTCTGATTGTATTAGGATTATTAATGGCATTATTTGGATTATCGCTTATCCGTGTATTTATAGtt                                                                          >  2:5660/1‑140 (MQ=255)

                                                        tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATCAtt                                                                          >  2:185568/1‑140 (MQ=255)

                                                          aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                        >  2:51397/1‑140 (MQ=255)

                                                              gTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTa                                                                    >  2:91572/1‑140 (MQ=255)

                                                                           tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                       >  2:435748/1‑140 (MQ=255)

                                                                             cAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaa                                                     <  2:331071/140‑1 (MQ=255)

                                                                                  aaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGAGTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcg                                                <  1:11798/140‑1 (MQ=255)

                                                                                   aaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTTGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                               <  2:122036/140‑1 (MQ=255)

                                                                                   aaGTAACACATCGCGTAAAAAGACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                               <  2:162352/140‑1 (MQ=255)

                                                                                    aGTACCACATCGCGTAAAAAAACCCACATCTATATCACTCAGAATATGTCTTACTGCACTAACACTACTAATGCCATTATTTGGATTATCACTTATCCTTCTATTTATAATTTAATTAATATTCTATTTTCATAAtcgtc                                              >  2:545899/1‑140 (MQ=255)

                                                                                         cacaTCGCGTACAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCt                                         <  1:772/140‑1 (MQ=255)

                                                                                          acaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                                        >  2:140509/1‑140 (MQ=255)

                                                                                                  tAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                                >  1:254096/1‑140 (MQ=255)

                                                                                                        aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                          <  1:192244/140‑1 (MQ=255)

                                                                                                                tCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGttt                  <  1:500980/140‑1 (MQ=255)

                                                                                                                    tatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGaa              >  1:251949/1‑140 (MQ=255)

                                                                                                                         cTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCTCTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAATATCGTTGTGCTAAACACTAATGCACGTAACGCTTTGCACTGAc         >  2:347740/1‑140 (MQ=255)

                                                                                                                           cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGa       >  2:43353/1‑140 (MQ=255)

                                                                                                                           cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTAGT‑CTAAACAATAATACACTTAAAATTTTGAACTGattaa      >  2:487004/1‑136 (MQ=255)

                                                                                                                           cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTACATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGa       >  1:326054/1‑140 (MQ=255)

                                                                                                                                tatGTTTTATTGTATTAGGATTATTAATTCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAGTAAATATCGTCGTTCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt  <  1:379433/140‑1 (MQ=255)

TTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513795‑1514062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A