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
A1 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,295,565	T→C	100%	F154F (TTT→TTC)	nrfE →	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,295,565	0	T	C	89.4%	195.9 / 11.6	66	F154F (TTT→TTC)	nrfE	heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE
Reads supporting (aligned to +/- strand): ref base T (6/1); new base C (28/31); total (34/32)
Fisher's exact test for biased strand distribution p-value = 1.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGGATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAG  >  W3110S.gb/4295497‑4295630

cGGATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 <  1:3454159/71‑1 (MQ=255)

cGGATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 <  1:152387/71‑1 (MQ=255)

cGGATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 <  1:2537396/71‑1 (MQ=255)

cGGATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 <  1:609123/71‑1 (MQ=255)

     atTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                            >  1:3491032/1‑71 (MQ=255)

     atTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCAc                                                            >  1:1917023/1‑71 (MQ=255)

          caccaGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgctg                                                       <  1:2242055/71‑1 (MQ=255)

              aGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCttt                                                   <  1:2506466/71‑1 (MQ=255)

              aGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCttt                                                   <  1:286168/71‑1 (MQ=255)

                    cGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTg                                             >  1:2277482/1‑71 (MQ=255)

                    cGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTg                                             >  1:1886064/1‑71 (MQ=255)

                    cGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTg                                             >  1:1786806/1‑71 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:2306750/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:3063953/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:2063670/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:1047626/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:2948639/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:1825210/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:2809856/71‑1 (MQ=255)

                      aaGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:2469288/71‑1 (MQ=255)

                       aGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGc                                           <  1:173467/70‑1 (MQ=255)

                       aGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCt                                          <  1:2957734/71‑1 (MQ=255)

                            gcgATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 >  1:2390184/1‑43 (MQ=255)

                            gcgATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 >  1:1479234/1‑43 (MQ=255)

                            gcgATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCa                                                                 >  1:2839369/1‑43 (MQ=255)

                              gATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCgg                                   >  1:1578852/1‑71 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCgctg                                                       >  1:2111759/1‑43 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:3694471/1‑71 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:40951/1‑71 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:2352128/1‑71 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:2917517/1‑71 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:2588347/1‑71 (MQ=255)

                                      tCCGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:1623189/1‑71 (MQ=255)

                                       ccGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATgg                           >  1:2862047/1‑70 (MQ=255)

                                        cGATGCTGCAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGt                          <  1:23803/70‑1 (MQ=255)

                                           tgctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcg                      >  1:2728575/1‑71 (MQ=255)

                                            gctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                         >  1:1227378/1‑51 (MQ=255)

                                            gctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                         >  1:1264162/1‑51 (MQ=255)

                                            gctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTa                                         >  1:550114/1‑51 (MQ=255)

                                             ctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcggc                    <  1:1443787/71‑1 (MQ=255)

                                             ctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcggc                    <  1:1257098/71‑1 (MQ=255)

                                             ctgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcggc                    <  1:2400740/71‑1 (MQ=255)

                                              tgcAACATCCCGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcggc                    <  1:2452944/70‑1 (MQ=255)

                                                     tCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg            >  1:2457302/1‑71 (MQ=255)

                                                     tCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg            <  1:1771106/71‑1 (MQ=255)

                                                      cccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCt                                          <  1:2734476/40‑1 (MQ=255)

                                                       ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCg               >  1:1068845/1‑66 (MQ=255)

                                                       ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCg               >  1:44249/1‑66 (MQ=255)

                                                       ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCg               >  1:2040979/1‑66 (MQ=255)

                                                       ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTgg            <  1:3023191/69‑1 (MQ=255)

                                                       ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGgcg          >  1:122317/1‑71 (MQ=255)

                                                       ccGGTCTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCAGCGAGCGTgg            <  1:1732862/69‑1 (MQ=255)

                                                            cTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAgcggc                    >  1:2642730/1‑56 (MQ=255)

                                                            cTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGc     >  1:3311882/1‑71 (MQ=255)

                                                            cTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGc     <  1:972376/71‑1 (MQ=255)

                                                            cTTATCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGAGGCGCTGGc     >  1:166641/1‑71 (MQ=255)

                                                               aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  >  1:2294164/1‑71 (MQ=255)

                                                               aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  >  1:1910059/1‑71 (MQ=255)

                                                               aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  >  1:1476568/1‑71 (MQ=255)

                                                               aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  >  1:735735/1‑71 (MQ=255)

                                                               aTCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  >  1:1204203/1‑71 (MQ=255)

                                                                tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  <  1:2372083/70‑1 (MQ=255)

                                                                tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  <  1:2094436/70‑1 (MQ=255)

                                                                tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  <  1:1863258/70‑1 (MQ=255)

                                                                tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  <  1:1390195/70‑1 (MQ=255)

                                                                tCTTCCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAg  <  1:888777/70‑1 (MQ=255)

CGGATATTTCCACCAGCAATCGAAGGCCGCGATCTCAATCCGATGCTGCAACATCCCGGTCTTATCTTTCATCCACCGCTGCTTTACCTTGGCTATGGCGGTTTGATGGTAGCGGCGAGCGTGGCGCTGGCGAG  >  W3110S.gb/4295497‑4295630

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A