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
A7 F28 I1 R1	172	67.8	2301510	98.9%	2276193	138.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,968,519	A→G	S153S (AGT→AGC)	rppH ←	RNA pyrophosphohydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,968,519	0	A	G	98.3%	202.5 / ‑4.3	60	S153S (AGT→AGC)	rppH	RNA pyrophosphohydrolase
Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (25/34); total (26/34)
Fisher's exact test for biased strand distribution p-value = 4.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.19e-01

GTGGTGCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACACTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTACTGCTGGTTTGCATATTGATTTCTGC  >  NC_000913/2968386‑2968653

gtggtgCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTcgcg                                                                                                                                  <  2:1086918/140‑1 (MQ=255)

  ggtgCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGaa                                                                                                                                >  1:1058118/1‑140 (MQ=255)

   gtgCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTcgcg                                                                                                                                  >  2:882395/1‑137 (MQ=255)

   gtgCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTcgcg                                                                                                                                  <  1:882395/137‑1 (MQ=255)

   gtgCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAAc                                                                                                                               >  1:997691/1‑140 (MQ=255)

   gtgCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAAc                                                                                                                               >  1:35990/1‑140 (MQ=255)

      cgcTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAActct                                                                                                                            >  2:640068/1‑140 (MQ=255)

        cTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCttt                                                                                                                          >  1:1060472/1‑140 (MQ=255)

           gCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCAt                                                                                                                       <  1:852636/140‑1 (MQ=255)

            cTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCAtt                                                                                                                      >  2:900487/1‑140 (MQ=255)

               ccTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTAcc                                                                                                                   <  2:1058118/140‑1 (MQ=255)

               ccTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTAcc                                                                                                                   <  1:881834/140‑1 (MQ=255)

                  tttCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTa                                                                                                                <  1:640068/140‑1 (MQ=255)

                     cGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCCCGCTCGCGAACTCTTTCATTCCCCGACgg                                                                                                             <  2:167837/140‑1 (MQ=255)

                     cGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTa                                                                                                                     <  2:574496/132‑1 (MQ=255)

                     cGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTa                                                                                                                     >  1:574496/1‑132 (MQ=255)

                     cGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTAcc                                                                                                                   <  2:1130148/134‑1 (MQ=255)

                     cGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTAcc                                                                                                                   >  1:1130148/1‑134 (MQ=255)

                     cGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACgg                                                                                                             >  2:593177/1‑140 (MQ=255)

                           tttCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACa                                                                                                       >  1:1054931/1‑140 (MQ=255)

                            ttCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACAt                                                                                                      <  1:1140472/140‑1 (MQ=255)

                            ttCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACAt                                                                                                      <  2:964150/140‑1 (MQ=255)

                            ttCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACAt                                                                                                      <  2:782944/140‑1 (MQ=255)

                             tCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATc                                                                                                     <  1:135910/140‑1 (MQ=255)

                              cgcgCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCa                                                                                                    >  2:67734/1‑140 (MQ=255)

                                    ggCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTa                                                                                              <  1:456057/140‑1 (MQ=255)

                                     gCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTaa                                                                                             >  1:212424/1‑140 (MQ=255)

                                     gCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTaa                                                                                             >  1:836958/1‑140 (MQ=255)

                                         gTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGa                                                                                         <  1:795964/140‑1 (MQ=255)

                                         gTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGa                                                                                         <  1:593177/140‑1 (MQ=255)

                                               aTAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATc                                                                                                     <  2:606102/122‑1 (MQ=255)

                                               aTAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATc                                                                                                     >  1:606102/1‑122 (MQ=255)

                                                 aaTTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGAcacca                                                                                    <  2:697502/137‑1 (MQ=255)

                                                 aaTTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGAcacca                                                                                    >  1:697502/1‑137 (MQ=255)

                                                   ttGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGt                                                                               <  1:900487/140‑1 (MQ=255)

                                                       cGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGa                                                                           <  1:67734/140‑1 (MQ=255)

                                                        gTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGAc                                                                          <  2:850737/140‑1 (MQ=255)

                                                         tGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGAcc                                                                         >  2:99845/1‑140 (MQ=255)

                                                           aCTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACGCCACCTGTCTGa                                                                           <  1:273067/136‑1 (MQ=255)

                                                           aCTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGa                                                                           >  2:273067/1‑136 (MQ=255)

                                                           aCTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCgg                                                                       >  1:856683/1‑140 (MQ=255)

                                                           aCTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCgg                                                                       >  1:888441/1‑140 (MQ=255)

                                                            cTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGa                                                                      <  1:99845/140‑1 (MQ=255)

                                                            cTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGa                                                                      <  2:1054931/140‑1 (MQ=255)

                                                                 ccTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCa                                                                 <  2:212424/140‑1 (MQ=255)

                                                                 ccTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCa                                                                 <  2:482849/140‑1 (MQ=255)

                                                                   tctTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGt                                                               <  2:856683/140‑1 (MQ=255)

                                                                     ttttACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTaa                                                             >  2:419411/1‑140 (MQ=255)

                                                                          cGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATAc                                                                   >  1:1086932/1‑129 (MQ=255)

                                                                          cGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATAc                                                                   <  2:1086932/129‑1 (MQ=255)

                                                                          cGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTAc                                                        <  2:848568/140‑1 (MQ=255)

                                                                                  aGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGcc                                                <  2:836958/140‑1 (MQ=255)

                                                                                         gCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTc                                         >  1:1079387/1‑140 (MQ=255)

                                                                                          cGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTc                                         <  1:302286/139‑1 (MQ=255)

                                                                                          cGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTc                                         >  2:302286/1‑139 (MQ=255)

                                                                                               tgtgGTTTTGGCGTATTTTCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTACCTTACCCATCGCCAGCCGTCCAActc                                   <  2:888441/140‑1 (MQ=255)

                                                                                                              ttttCCTGCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTACTGCTGGt                    <  1:526428/140‑1 (MQ=255)

                                                                                                                     gCAGTGACATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCTGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTACTGCTGGTTTGCata             <  2:1060472/140‑1 (MQ=255)

                                                                                                                           aCATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTActg                         >  2:10162/1‑122 (MQ=255)

                                                                                                                           aCATCACCACGCTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTActg                         <  1:10162/122‑1 (MQ=255)

                                                                                                                                accacACTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTACTGCTGGTTTGCATATTGATTTCTGc  >  1:836762/1‑140 (MQ=255)

GTGGTGCGCTGGCTACCTTTTCGACTATTTCGCGCAGGCGAGTGAGCATAATTGGCGTGACTTAACCTCTTTTACGTCGATAAGCAGATGCGTTTTGTGGTTTTGGCGTATTTTCCTGCAGTGACATCACCACACTCGCGAACTCTTTCATTACCCTACGGTAGACATCACGTTTAAATGACACCACCTGTCTGACCGGATACCAGTAACTTACCCATCGCCAGCCGTCAAACTCTGGTGTACTGCTGGTTTGCATATTGATTTCTGC  >  NC_000913/2968386‑2968653

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A