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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,639,499	G→A	53.7%	D180D (GAC→GAT)	ypfH ←	predicted hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,639,499	0	G	A	53.7%	12.9 / 107.3	123	D180D (GAC→GAT)	ypfH	predicted hydrolase
Reads supporting (aligned to +/- strand): ref base G (41/16); new base A (24/42); total (65/58)
Fisher's exact test for biased strand distribution p-value = 1.24e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

Only 100 of 134 total aligned reads displayed.

CCAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAACCGGATCTTC  >  minE/1639432‑1639567

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGcgtcacgt                                                                     >  1:1016674/1‑69 (MQ=255)

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGcgtcacgt                                                                     >  1:3323184/1‑69 (MQ=255)

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGcgtcacgt                                                                     >  1:3017496/1‑69 (MQ=255)

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGcgtcacgt                                                                     >  1:2473003/1‑69 (MQ=255)

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGcgtcacgt                                                                     >  1:123894/1‑69 (MQ=255)

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGcgtcacgt                                                                     >  1:2367373/1‑69 (MQ=255)

ccAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCCCCACGATATCCAGcgtcacg                                                                      >  1:3210147/1‑68 (MQ=255)

          ttGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGc                                                           >  1:468576/1‑69 (MQ=255)

          ttGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGc                                                           >  1:2938599/1‑69 (MQ=255)

          ttGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGc                                                           >  1:2518218/1‑69 (MQ=255)

           tGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCa                                                          <  1:926792/69‑1 (MQ=255)

           tGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCa                                                          <  1:3054722/69‑1 (MQ=255)

           tGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCa                                                          <  1:2031905/69‑1 (MQ=255)

            gCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCa                                                          >  1:1010454/1‑68 (MQ=255)

            gCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCa                                                          >  1:2185864/1‑68 (MQ=255)

            gCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCa                                                          >  1:1201884/1‑68 (MQ=255)

                 cTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCAGTGAtt                                                    <  1:196211/69‑1 (MQ=255)

                 cTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGAtt                                                    <  1:953002/69‑1 (MQ=255)

                 cTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGAtt                                                    <  1:1594518/69‑1 (MQ=255)

                 cTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGAtt                                                    <  1:2250992/69‑1 (MQ=255)

                 cTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGAtt                                                    <  1:2632185/69‑1 (MQ=255)

                 cTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGAtt                                                    <  1:179986/69‑1 (MQ=255)

                   gCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTaa                                                  >  1:1893257/1‑69 (MQ=255)

                   gCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTaa                                                  >  1:2523347/1‑69 (MQ=255)

                   gCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTaa                                                  >  1:2590666/1‑69 (MQ=255)

                   gCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTaa                                                  >  1:1860153/1‑69 (MQ=255)

                   gCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTaa                                                  >  1:3383256/1‑69 (MQ=255)

                      aTTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCCCCACCGGCACTGATTAACGc                                               >  1:1976080/1‑69 (MQ=255)

                      aTTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGc                                               >  1:2158737/1‑69 (MQ=255)

                      aTTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGc                                               >  1:3247739/1‑69 (MQ=255)

                      aTTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGc                                               >  1:2996548/1‑69 (MQ=255)

                               cGCATGGCCTAAATCCTCCACGATATCCAGCGTCTCGTCACCACCGGCACTGATTAACGCTTCCTgcgc                                      <  1:2829792/69‑1 (MQ=255)

                               cGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTgcgc                                      <  1:1509313/69‑1 (MQ=255)

                               cGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTgcgc                                      >  1:1040749/1‑69 (MQ=255)

                                   tGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGcgccgc                                   >  1:3106437/1‑68 (MQ=255)

                                   tGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCa                                  >  1:1009909/1‑69 (MQ=255)

                                     gCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAAc                                >  1:2010454/1‑69 (MQ=255)

                                     gCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAAc                                >  1:567609/1‑69 (MQ=255)

                                     gCCTAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCaa                                 >  1:2606451/1‑68 (MQ=255)

                                     gCCTAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCa                                  >  1:2304700/1‑67 (MQ=255)

                                     gCCTAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAAc                                >  1:1125362/1‑69 (MQ=255)

                                     gCCTAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAAc                                >  1:1737462/1‑69 (MQ=255)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:2975652/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:297414/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:1474235/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:557227/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:310132/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:2575962/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:719032/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:128739/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:1860893/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:1653523/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:1793292/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:1350408/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:1703907/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:2148866/48‑1 (MQ=38)

                                        tAAATCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:2032976/48‑1 (MQ=38)

                                        tAAATCCTCCACGAAATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:2355611/48‑1 (MQ=37)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1093280/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1919510/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1380896/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1075316/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:3227988/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1071312/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:2161785/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:475935/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:560951/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:2290157/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1587109/69‑1 (MQ=255)

                                         aaaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:2407511/69‑1 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:524279/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:3093278/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:1445685/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:308498/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:2290031/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCCCCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:2215926/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCt                                              >  1:3223027/1‑50 (MQ=39)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACGGCAt                           >  1:3015005/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            >  1:2952367/1‑68 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:488591/68‑1 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCa                            <  1:1672212/68‑1 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:2931104/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:2546147/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:1684049/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:2857124/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:2857502/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:1110672/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCAt                           >  1:3192263/1‑69 (MQ=255)

                                          aaTCCTCCACGATATCCAGCGTCACATCGCCACCGGCACTGATTAACGCTTCCTGCCCCGCAACCGCAt                           >  1:3271457/1‑69 (MQ=255)

                                             cctccACGATATCCAGCGTCACGTCACCACCGGGACTGATTAACGCTTCCTGCGCCGCAACCGCATgc                         >  1:3076616/1‑68 (MQ=255)

                                             cctccACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATgc                         >  1:313028/1‑68 (MQ=255)

                                             cctccACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATgc                         >  1:1656388/1‑68 (MQ=255)

                                              ctccACGATATCCAGCGTCACATCGCCACCGGCACTGATTaa                                                  <  1:2293015/42‑1 (MQ=38)

                                                        tCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATa             <  1:582785/69‑1 (MQ=255)

                                                          cAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAAc           >  1:1093751/1‑69 (MQ=255)

                                                          cAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAAc           >  1:2568496/1‑69 (MQ=255)

                                                          cAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAAc           >  1:318089/1‑69 (MQ=255)

                                                          cAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAAc           >  1:1784820/1‑69 (MQ=255)

                                                                   gtcacCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAACCGGATCTTc  <  1:162373/69‑1 (MQ=255)

                                                                   gtcacCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAACCGGATCTTc  <  1:2370565/69‑1 (MQ=255)

CCAGGGCAAATTGCATACTGCGATTGTCGATCGCATGGCCTAAATCCTCCACGATATCCAGCGTCACGTCACCACCGGCACTGATTAACGCTTCCTGCGCCGCAACCGCATGCGCCAGATCGATAACCGGATCTTC  >  minE/1639432‑1639567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A