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
A4 F28 I1 R1	159	82.1	2830106	99.3%	2810295	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,962,491	(C)_5→6	coding (274/324 nt)	ppdC ←	putative YgdA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,962,486	1	.	C	97.9%	165.0 / ‑3.4	47	coding (279/324 nt)	ppdC	putative YgdA
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (26/20); total (26/21)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCCAGCCGTTCGCGTTCGACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TG‑CCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATGCCGCCAGAGCTG  >  NC_000913/2962347‑2962620

cGTCCAGCCGTTCGCGTTCGACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑Tg                                                                                                                                         <  2:1319057/140‑1 (MQ=255)

 gTCCAGCCGTTCGCGTTCGACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TG‑c                                                                                                                                       <  1:827007/140‑1 (MQ=255)

   ccAGCCGTTCGCGTTCGACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TG‑ccc                                                                                                                                     <  2:1134350/140‑1 (MQ=255)

    cAGCCGTTCGCGTTCGACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TG‑cccc                                                                                                                                    <  1:161294/140‑1 (MQ=255)

          ttcgcgttcgACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TG‑CCCCCcgggt                                                                                                                              <  2:492660/140‑3 (MQ=255)

               gttcgACAATAAACTCCATTAACGCTTCCAGCACGTCCAGACGATTGGAGTGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAAc                                                                                                                          <  2:949086/140‑1 (MQ=255)

                  cgACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAg                                                                                                                       >  2:241721/1‑140 (MQ=255)

                             tCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGa                                                                                                            >  1:517815/1‑140 (MQ=255)

                               gacagaCGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATg                                                                                                          <  1:754438/135‑1 (MQ=255)

                               cATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATg                                                                                                          >  1:1192909/1‑140 (MQ=255)

                               cATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATg                                                                                                          <  1:241721/140‑1 (MQ=255)

                                 tCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCt                                                                                                        >  1:1205149/1‑140 (MQ=255)

                                    aCGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGac                                                                                                     >  1:1030562/1‑140 (MQ=255)

                                         tCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATc                                                                                                <  1:429865/140‑1 (MQ=255)

                                            aGCACGTGCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCg                                                                                             <  1:1311864/140‑1 (MQ=255)

                                             gCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGc                                                                                            <  2:1192909/140‑1 (MQ=255)

                                               aCGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGGCATCTCGCCTTCTC‑TGCCCCCCCGGGGAAACTAGCGTAACGCTGATGCTGACACATccctgtc                                                                                          >  2:754438/1‑136 (MQ=255)

                                                 gTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGc                                                                                        <  2:574014/140‑1 (MQ=255)

                                                  tCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCg                                                                                       >  1:433520/1‑140 (MQ=255)

                                                  tCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCg                                                                                       >  1:1351592/1‑140 (MQ=255)

                                                  tCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCCGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCg                                                                                       >  1:169820/1‑140 (MQ=255)

                                                   ccAGACGATTGGAATGGTAGACCCTTAACATAGTGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGa                                                                                      <  1:453894/140‑1 (MQ=255)

                                                                        cccTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGAc                                                                    >  2:1166391/1‑137 (MQ=255)

                                                                        cccTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGAc                                                                    <  1:1166391/137‑1 (MQ=255)

                                                                        cccTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTg                                                                 >  2:83635/1‑140 (MQ=255)

                                                                         ccTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGc                                                                <  2:357753/140‑1 (MQ=255)

                                                                         ccTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGc                                                                >  2:233280/1‑140 (MQ=255)

                                                                              aCATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAAATAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGtt                                                           >  2:1152318/1‑140 (MQ=255)

                                                                                aTAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTgg                                                         <  1:831412/140‑1 (MQ=255)

                                                                                  aGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCa                                                       <  2:55874/140‑1 (MQ=255)

                                                                                  aGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCa                                                       >  2:1065951/1‑140 (MQ=255)

                                                                                   gCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAg                                                      >  1:323238/1‑140 (MQ=255)

                                                                                   gCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCCGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAg                                                      >  2:661852/1‑140 (MQ=255)

                                                                                    cGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGGTGACAAATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAgg                                                     >  1:232333/1‑140 (MQ=255)

                                                                                       cTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCCGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCCCCCGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTgg                                                  >  2:417190/1‑140 (MQ=255)

                                                                                         ccTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCg                                                >  2:1210819/1‑140 (MQ=255)

                                                                                         ccTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCg                                                >  2:1020868/1‑140 (MQ=255)

                                                                                              ctactGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATc                                           <  2:1351592/140‑1 (MQ=255)

                                                                                                 ctGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATcgcg                                        <  1:661852/140‑1 (MQ=255)

                                                                                                 ctGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCCGGTGAAACTAGCGTAACGCTGGTGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATcgcg                                        >  1:1383180/1‑140 (MQ=255)

                                                                                                   gACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATcgcgcg                                      <  1:1020868/140‑1 (MQ=255)

                                                                                                         tCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTg                                >  1:501403/1‑140 (MQ=255)

                                                                                                             gCAATGCAGGCGGGTCTTCTCGCCTTCTCGCC‑CCCCCGGTTGAAACTAGCGTACCGCTGATGCTTACACTTCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGtt                            <  2:942857/140‑1 (MQ=255)

                                                                                                                      gCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTgccag                   >  2:622916/1‑140 (MQ=255)

                                                                                                                      gCGGGTCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTgccag                   >  1:6990/1‑140 (MQ=255)

                                                                                                                           tCATCTCGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATg              >  1:1129100/1‑140 (MQ=255)

                                                                                                                           tCATCTCGCCTTCTC‑TGCCCCCCGGGGGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATg              >  2:1336518/1‑140 (MQ=255)

                                                                                                                               ctcGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATgccgc          <  2:433520/140‑1 (MQ=255)

                                                                                                                               ctcGCCTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATgccac          <  1:625374/140‑3 (MQ=255)

                                                                                                                                   ccTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATGCCGCCaga      <  2:517815/140‑1 (MQ=255)

                                                                                                                                    cTTCTC‑TGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATGCCGCCagag     <  2:323238/140‑1 (MQ=255)

                                                                                                                                       ctc‑tGCCCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATGCCGCCAGAGCTg  <  1:366144/140‑1 (MQ=255)

CGTCCAGCCGTTCGCGTTCGACAATAAACTCCATCAACGCTTCCAGCACGTCCAGACGATTGGAATGGTAGACCCTTAACATAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCGGGTCATCTCGCCTTCTC‑TG‑CCCCCGGGTGAAACTAGCGTAACGCTGATGCTGACACATCCCGCCTGCGATGTCTGCATTCGGTTGACCTGCCAGTTGGCAGGTGGCGAAATCGCGCGCAGTTGCGTTTGCTGCCAGCCATGCCGCCAGAGCTG  >  NC_000913/2962347‑2962620

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A