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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,571,344:1	+A	16.9%	intergenic (+112/‑1667)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,571,344	1	.	A	16.9%	167.7 / 44.2	59	intergenic (+112/‑1667)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base . (18/31); new base A (5/5); total (23/36)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

ATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCG  >  minE/2571277‑2571411

attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑Tg                                                                   <  1:2119564/70‑1 (MQ=255)

 ttattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGa                                                                 <  1:1232140/71‑1 (MQ=255)

 ttattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGa                                                                 <  1:2225942/71‑1 (MQ=255)

  tattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGAt                                                                >  1:85200/1‑71 (MQ=255)

  tattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGAt                                                                >  1:2182597/1‑71 (MQ=255)

  tattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGAt                                                                >  1:418124/1‑71 (MQ=255)

   attTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGAt                                                                >  1:2254309/1‑70 (MQ=255)

    tttttGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATg                                                               <  1:3533469/70‑1 (MQ=255)

      tttGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAg                                                             <  1:2502571/70‑1 (MQ=255)

        tGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAgtg                                                           <  1:2389877/70‑1 (MQ=255)

         gCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAgtgt                                                          >  1:1360047/1‑70 (MQ=255)

           atatTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTAct                                                       <  1:2694549/71‑1 (MQ=255)

              ttACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGctct                                                     <  1:175902/70‑1 (MQ=255)

                aCTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCa                                                   <  1:3027968/70‑1 (MQ=255)

                aCTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCa                                                   <  1:1985376/70‑1 (MQ=255)

                 cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCAtt                                                 <  1:2485622/71‑1 (MQ=255)

                    cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGa                                                                 >  1:1637292/1‑52 (MQ=255)

                    cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTg                                                <  1:2992931/69‑1 (MQ=255)

                    cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGa                                              >  1:2008979/1‑71 (MQ=255)

                     aTTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGGGTGCTCTCATTGGAt                                             <  1:2791507/71‑1 (MQ=255)

                      ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑Tg                                                                   <  1:909931/48‑1 (MQ=255)

                      ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑Tg                                                                   <  1:1884285/48‑1 (MQ=255)

                        aGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGa                                                                 >  1:2105731/1‑48 (MQ=255)

                          cTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGAtttttt                                        <  1:51191/71‑1 (MQ=255)

                          cTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGAtttttt                                        <  1:1809107/71‑1 (MQ=255)

                          cTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGAtttttt                                        <  1:1410050/71‑1 (MQ=255)

                            tCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAgt                                                            >  1:1241951/1‑49 (MQ=255)

                            tCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAgt                                                            >  1:2625243/1‑49 (MQ=255)

                            gtgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTC‑t                                                                    >  1:1733264/3‑42 (MQ=12)

                            gtgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTC‑Tg                                                                   >  1:2571275/3‑43 (MQ=16)

                             cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATc                                     >  1:466854/1‑71 (MQ=255)

                              gatgatTTTTCCTTTAATATCCAGCATGTAAAGAAGTTc                                                                      >  1:2962167/1‑39 (MQ=9)

                               atgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCg                                   <  1:1035998/71‑1 (MQ=255)

                                tgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATcc                                    >  1:602030/1‑71 (MQ=255)

                                 gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                                 >  1:334079/1‑71 (MQ=255)

                                  atTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                                 <  1:833991/70‑1 (MQ=255)

                                       tccTTTAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATCCGTc                                 >  1:1663272/3‑67 (MQ=255)

                                       tccTTTAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                              <  1:1699436/68‑1 (MQ=255)

                                        ccTTTAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTga                             <  1:2002593/69‑2 (MQ=255)

                                         cTTTAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTACCCGTCTTGATc                           <  1:681628/71‑1 (MQ=255)

                                         atttAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                           >  1:1204721/2‑71 (MQ=255)

                                           ttAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTg                         >  1:1385251/1‑71 (MQ=255)

                                            tAATATCCAGCATGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTgt                        >  1:3859165/1‑70 (MQ=255)

                                               tatTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGAt                                             <  1:2954658/46‑1 (MQ=255)

                                               tatTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTAACCGTCTTGTTCTGCCGc                     <  1:1658843/70‑1 (MQ=255)

                                                    aTTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                <  1:2701468/70‑1 (MQ=255)

                                                    aTTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                <  1:3677991/70‑1 (MQ=255)

                                                     ttATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga              <  1:2009661/71‑1 (MQ=255)

                                                     gcaTGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTa                                       <  1:3193494/45‑1 (MQ=255)

                                                     gcaTGTTAAGAAGTTCAGGGATAGCTGTGATCTCATTGGATTTCTTa                                       <  1:3041316/45‑1 (MQ=255)

                                                      tATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTc                           >  1:779794/1‑57 (MQ=255)

                                                      tATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGa                 >  1:2418661/1‑67 (MQ=255)

                                                       aTGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATgag             <  1:3209317/70‑1 (MQ=255)

                                                        tGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGAc           >  1:355609/1‑71 (MQ=255)

                                                          ttAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACt          <  1:209001/70‑1 (MQ=255)

                                                          ttAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACt          <  1:3269259/70‑1 (MQ=255)

                                                            aataaGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtat        <  1:257301/70‑1 (MQ=255)

                                                             ataaGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata       <  1:2815788/70‑1 (MQ=255)

                                                              taaGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACa     >  1:13632/1‑71 (MQ=255)

                                                               aaGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAt    >  1:3522116/1‑71 (MQ=255)

                                                                 gTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcg  <  1:1944225/71‑1 (MQ=255)

ATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑TGGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCG  >  minE/2571277‑2571411

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A