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
A17 F48 I1 R1	90	35.3	1199032	98.5%	1181046	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	641,517	C→A	S117S (TCG→TCT)	uspG ←	universal stress protein G

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	641,517	0	C	A	96.8%	97.4 / ‑3.8	31	S117S (TCG→TCT)	uspG	universal stress protein G
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (13/17); minor base G (1/0); total (14/17)
Fisher's exact test for biased strand distribution p-value = 4.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

AAGCCCCGCCGGGATGGCTCCGGGCAGGGCGGGATACTTATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATCGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGATGGTGAAGTGGCTGACCA  >  NC_000913/641390‑641650

aaGCCCCGCCGGGATGGCTCCGGGCAGGGCGGGATACTTATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCga                                                                                                                           <  2:446650/140‑1 (MQ=255)

   ccccGCCGGGATGGCTCCGGGCAGGGCGGGATACTTATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGaa                                                                                                                        <  2:377612/140‑1 (MQ=255)

         cgGGATGGCTCCGGGCAGGGCGGGATACTTATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATa                                                                                                                  <  2:591436/140‑1 (MQ=255)

                            gCGGGATACTTATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCa                                                                                               >  1:432195/1‑140 (MQ=255)

                                     ttATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTg                                                                                      >  2:8489/1‑140 (MQ=255)

                                     ttATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTg                                                                                      >  1:439957/1‑140 (MQ=255)

                                     ttATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGGTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTg                                                                                      >  1:289192/1‑140 (MQ=255)

                                       aTTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGcc                                                                                    <  2:439957/140‑1 (MQ=255)

                                        ttCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCa                                                                                   >  1:311513/1‑140 (MQ=255)

                                              taaTTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGTTCACGCCCGAGGCTTTAGAACCCAACAGATGGGTCGAAATAGATGGGGTGCGAGAACCAATAACTGCAACATCAGCCCCCAGTTCTTCTGCCAACACAt                                                                             >  2:263525/2‑140 (MQ=255)

                                                  tAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCCTTAGAATCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTTCTAACTCATTCAc                                                                         >  2:504034/1‑140 (MQ=255)

                                                         caACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCAttc                                                                  <  1:328660/140‑3 (MQ=255)

                                                              aGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCAc                                                             >  2:310957/1‑140 (MQ=255)

                                                              aGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCAc                                                             <  1:569797/140‑1 (MQ=255)

                                                                   cGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTAc                                                        <  1:328787/140‑1 (MQ=255)

                                                                    ggCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTAcc                                                       >  1:88637/1‑140 (MQ=255)

                                                                      cAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCaa                                                     >  1:159772/1‑140 (MQ=255)

                                                                      cAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCaa                                                     >  1:256458/1‑140 (MQ=255)

                                                                        gATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCaaaa                                                   >  1:377660/1‑140 (MQ=255)

                                                                          ttGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGTTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACg                                                 >  1:409510/1‑140 (MQ=255)

                                                                             gcgtggcgGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGAc                                              <  1:109917/140‑1 (MQ=255)

                                                                                         aCGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAAt                                  <  2:289192/140‑1 (MQ=255)

                                                                                             tCGAGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCgg                              <  1:8489/140‑1 (MQ=255)

                                                                                                aGGCGTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAG‑CCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAg                          >  2:394525/1‑140 (MQ=255)

                                                                                                    gTTAGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGAt                       <  2:37779/140‑1 (MQ=255)

                                                                                                       aGAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGa                    <  2:119329/140‑1 (MQ=255)

                                                                                                        gAACCTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGAt                   <  2:256458/140‑1 (MQ=255)

                                                                                                            cTAACAGATGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGATGGTg               <  1:310957/140‑1 (MQ=255)

                                                                                                                   aTGGGTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACAACAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGATGGTGAAGTGGc        <  1:263525/140‑1 (MQ=255)

                                                                                                                     gggTCGAAATGGATGGGGTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGTCATGTTGTTTAATGCGGGAAGGATCGATGGTGAATTGGCTg      >  2:85053/1‑140 (MQ=255)

                                                                                                                     gagacGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCATCCCCCAGTTCTTCTGCCAACTCATTGACTTAATCCCGCACGCTACCAAATCGGACATGTTGTTTAATGCGGGAAGGATCGATGGTGAAGTGGCTg      >  2:310068/5‑140 (MQ=255)

                                                                                                                      ggTCGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGATGGTGAAGTGGCTGa     <  1:527984/140‑1 (MQ=255)

                                                                                                                         cGAAATAGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGATGGTGAAGTGGCTGACCa  <  2:406505/140‑1 (MQ=255)

AAGCCCCGCCGGGATGGCTCCGGGCAGGGCGGGATACTTATTCTGGCAATTAACGCACAACCAGCACCGGCAGATTGGCGTGGCGGATCACGCTCGAGGCGTTAGAACCTAACAGATGGGTCGAAATCGATGGGTTGCGAGAACCAATAACTACAACATCAGCCCCCAGTTCTTCTGCCAACTCATTGACTTCATCCCGCACGCTACCAAAACGGACATGTTGTTTAATGCGGGAAGGATCGATGGTGAAGTGGCTGACCA  >  NC_000913/641390‑641650

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A