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
A5 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	833,307	G→T	45.3%	T22T (ACC→ACA)	ybiA ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	833,307	0	G	T	45.3%	61.2 / 67.2	64	T22T (ACC→ACA)	ybiA	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (21/14); new base T (10/19); total (31/33)
Fisher's exact test for biased strand distribution p-value = 4.92e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.80e-01

CAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTA  >  W3110S.gb/833242‑833374

cAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGc                                                                 >  1:2892772/1‑70 (MQ=255)

cAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCt                                                                <  1:100515/71‑1 (MQ=255)

 aGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTg                                                               >  1:385840/1‑71 (MQ=255)

    ttttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAg                                                            <  1:1565913/71‑1 (MQ=255)

     tttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAg                                                            >  1:3258263/1‑70 (MQ=255)

     tttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAg                                                            >  1:597304/1‑70 (MQ=255)

     tttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTa                                                             >  1:3587999/1‑69 (MQ=255)

     tttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAg                                                            >  1:1696896/1‑70 (MQ=255)

     tttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAg                                                            >  1:1151857/1‑70 (MQ=255)

      ttCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGa                                                           <  1:2509516/70‑1 (MQ=255)

             cAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTat                                                    >  1:4148988/1‑70 (MQ=255)

             cAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTat                                                    >  1:2902083/1‑70 (MQ=255)

                    gATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTatgatg                                                <  1:1619366/67‑1 (MQ=255)

                      tGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAAtt                                                       <  1:1489738/58‑1 (MQ=255)

                        ggCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCtt                                         <  1:4742878/70‑1 (MQ=255)

                        ggCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTg                                        <  1:2252050/71‑1 (MQ=255)

                          ccAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTa                                                     >  1:1308134/1‑56 (MQ=255)

                          ccAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTa                                                     >  1:779301/1‑56 (MQ=255)

                           cAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCAt                                     <  1:3881196/71‑1 (MQ=255)

                            aGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCAt                                     <  1:3012667/70‑1 (MQ=255)

                             ggcggcAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCAt                                     <  1:3287212/69‑1 (MQ=255)

                              gcggcAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTg                                                               <  1:490002/42‑1 (MQ=255)

                              gcggcAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATgg                                               >  1:3231161/1‑58 (MQ=255)

                               cggcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGgt                                              >  1:3993063/1‑58 (MQ=255)

                               cggcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGgt                                              >  1:11637/1‑58 (MQ=255)

                                ggcAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTa                                                             >  1:262971/1‑42 (MQ=255)

                                ggcAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACgt                                >  1:3246833/1‑71 (MQ=255)

                                ggcAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACgt                                <  1:1515470/71‑1 (MQ=255)

                                 gcAAAGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACgtg                               <  1:168092/71‑1 (MQ=255)

                                   aaaGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGtt                             >  1:5102079/1‑71 (MQ=255)

                                    aaGTTAGAAAAATCACCGTAGTCATCGCTTGTGCt                                                                <  1:5083246/35‑1 (MQ=255)

                                    aaGTTAGAAAAATCACCGTAGTCATCGCTTGTGCt                                                                <  1:762709/35‑1 (MQ=255)

                                    aaGTTAGAAAAATCACCGTAGTCATCGCTTGTGCt                                                                <  1:1089189/35‑1 (MQ=255)

                                    aaGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGgtgt                                            <  1:3255989/55‑1 (MQ=255)

                                     aGTTAGAAAAATCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTgg                           <  1:1519817/71‑1 (MQ=255)

                                         aGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTg                            >  1:4947780/1‑66 (MQ=255)

                                           aaaaaTCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCtt                     <  1:2655965/71‑1 (MQ=255)

                                            aaaaTCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCtt                     <  1:952870/70‑1 (MQ=255)

                                             aaaTCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGAc                                  >  1:2209352/1‑56 (MQ=255)

                                             aaaTCACCGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTtg                   >  1:2722293/1‑71 (MQ=255)

                                             aaaTCACCGTAGTCATCGCTGGTGCTGTAGAAATTTatgatg                                                >  1:3111059/1‑42 (MQ=255)

                                             aaaTCACCGTAGTCATCGCTGGTGCTGTAGAAATTTatgatg                                                >  1:1393436/1‑42 (MQ=255)

                                                tCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGc                <  1:1085560/71‑1 (MQ=255)

                                                   ccGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCg             <  1:4371348/71‑1 (MQ=255)

                                                   ccGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCg             <  1:2937896/71‑1 (MQ=255)

                                                    cGTAGTCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGAT‑CTTTTTGCTCGaa           <  1:2327721/71‑1 (MQ=255)

                                                         tCATCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACggg       <  1:431062/71‑1 (MQ=255)

                                                         tCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACggg       <  1:2086901/71‑1 (MQ=255)

                                                         tCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACggg       <  1:4393984/71‑1 (MQ=255)

                                                          cATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACggg       >  1:1051818/1‑70 (MQ=255)

                                                           aTCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCg             >  1:4257934/1‑63 (MQ=255)

                                                            tCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCt                      <  1:1627606/53‑1 (MQ=255)

                                                            tCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCt                      <  1:597370/53‑1 (MQ=255)

                                                            tCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCt                      <  1:4644321/53‑1 (MQ=255)

                                                            tCGCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCt                      <  1:3484874/53‑1 (MQ=255)

                                                              gCTTGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTa  <  1:998747/71‑1 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGa                                   >  1:4071639/1‑38 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGa                                   >  1:3026077/1‑38 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGa                                   >  1:1705183/1‑38 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTgg                           >  1:3617190/1‑46 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCttt                    >  1:4596131/1‑53 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCttt                    >  1:853309/1‑53 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCttt                    >  1:1025342/1‑53 (MQ=255)

                                                              gCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTa  <  1:3388190/71‑1 (MQ=255)

CAGGTTTTCCCGTCAACCTTGATGGGCCAGGCGGCAAAGTTAGAAAAATCACCGTAGTCATCGCTGGTGCTGTAGAAATTTATGATGGTGTCTTGCATGACGTGTTGGATCCTTTGTGCTCGAACGGGCATTA  >  W3110S.gb/833242‑833374

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