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 R1	311	50.1	4085234	95.9%	3917739	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,211,677	C→T	41.2%	intergenic (+169/‑26)	dnaG → / → rpoD	DNA primase/RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,211,677	0	C	T	41.2%	51.3 / 94.2	80	intergenic (+169/‑26)	dnaG/rpoD	DNA primase/RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand): ref base C (19/28); new base T (14/19); total (33/47)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCG  >  W3110S.gb/3211610‑3211746

gTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCAt                                                                     >  1:4047924/1‑70 (MQ=255)

  aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGa                                                                   >  1:3221886/1‑70 (MQ=255)

  aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGa                                                                   >  1:1693607/1‑70 (MQ=255)

  aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGa                                                                   >  1:1425243/1‑70 (MQ=255)

   aacaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGaaa                                                                 <  1:1307734/71‑1 (MQ=255)

   aacaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGaaa                                                                 >  1:249210/1‑71 (MQ=255)

    acaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                                <  1:3980714/71‑1 (MQ=255)

    acaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                                <  1:1505456/71‑1 (MQ=255)

     caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATa                                                               <  1:2381720/71‑1 (MQ=255)

     caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                                >  1:991787/1‑70 (MQ=255)

     caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                                >  1:3029764/1‑70 (MQ=255)

       acCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAg                                                             <  1:3993434/71‑1 (MQ=255)

        ccGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAgt                                                            <  1:417399/71‑1 (MQ=255)

         cGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAgtg                                                           <  1:2521666/71‑1 (MQ=255)

         cGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAgtg                                                           <  1:1122992/71‑1 (MQ=255)

           ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGtgtg                                                         <  1:2271682/71‑1 (MQ=255)

           ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGtgtg                                                         <  1:2036103/71‑1 (MQ=255)

           ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                         <  1:507127/71‑1 (MQ=255)

           ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                         <  1:3035011/71‑1 (MQ=255)

           ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                         <  1:2014347/71‑1 (MQ=255)

             ggATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                       >  1:2125241/1‑71 (MQ=255)

                 ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                       >  1:3946802/1‑67 (MQ=255)

                 ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                       >  1:2852968/1‑67 (MQ=255)

                 ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                       >  1:2272574/1‑67 (MQ=255)

                 ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                       >  1:3797212/1‑67 (MQ=255)

                 ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATAcc                                                   >  1:844597/1‑71 (MQ=255)

                     gCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCt                                               >  1:1437764/1‑71 (MQ=255)

                     gCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCt                                               >  1:2618710/1‑71 (MQ=255)

                     gCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCt                                               >  1:247752/1‑71 (MQ=255)

                      cGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCt                                               <  1:807406/70‑1 (MQ=255)

                       gTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                             <  1:829391/71‑1 (MQ=255)

                       gTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                             <  1:1722/71‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                                <  1:623302/51‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATa                                                               <  1:3657449/52‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATa                                                               <  1:2125196/52‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATa                                                               <  1:2957706/52‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATa                                                               <  1:3499320/52‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg                                                             <  1:2369927/54‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg                                                             <  1:1177603/54‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg                                                             <  1:2216098/54‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg                                                             <  1:2163256/54‑1 (MQ=255)

                        ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTAt                                            >  1:1738077/1‑71 (MQ=255)

                                    ggACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                         <  1:1215071/46‑1 (MQ=255)

                                    ggACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                         <  1:2678449/46‑1 (MQ=255)

                                    ggACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                         <  1:1966607/46‑1 (MQ=255)

                                       cATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg                               >  1:2412127/1‑69 (MQ=255)

                                       cATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg                               >  1:432819/1‑69 (MQ=255)

                                       cATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg                               >  1:975012/1‑69 (MQ=255)

                                        aTCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGtgtg                                                         <  1:2810544/42‑1 (MQ=255)

                                         tCGGGTCAATCGCCCAACACCAACCTTATGAAATa                                                               <  1:535896/35‑1 (MQ=255)

                                         tCGGGTCAATCGCCCAACACCAACCTTATGAAATa                                                               <  1:321020/35‑1 (MQ=255)

                                           gggTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca                         >  1:1838462/1‑71 (MQ=255)

                                           gggTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca                         >  1:3250288/1‑71 (MQ=255)

                                              tCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcac                        <  1:1374129/69‑1 (MQ=255)

                                              tCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcac                        <  1:3614207/69‑1 (MQ=255)

                                              tCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATgg                                          <  1:1141288/51‑1 (MQ=255)

                                                 aTCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTa                                             <  1:2724570/45‑1 (MQ=255)

                                                 aTCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTa                                             <  1:2233591/45‑1 (MQ=255)

                                                  tCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGa                  <  1:1706179/71‑1 (MQ=255)

                                                    gCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa                                   >  1:1075477/1‑52 (MQ=255)

                                                    gCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa                                   >  1:3203965/1‑52 (MQ=255)

                                                    gCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa                                   >  1:3114640/1‑52 (MQ=255)

                                                      ccAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAAc               <  1:3065094/70‑1 (MQ=255)

                                                       cAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActt             <  1:983455/71‑1 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                             <  1:128751/38‑1 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                             <  1:1414577/38‑1 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                             <  1:104501/38‑1 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                             <  1:2754299/38‑1 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtc            >  1:768888/1‑71 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtc            >  1:3959441/1‑71 (MQ=255)

                                                        aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtc            <  1:3428388/71‑1 (MQ=255)

                                                           acCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTg         >  1:2850800/1‑71 (MQ=255)

                                                            ccAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGt        <  1:3979375/71‑1 (MQ=255)

                                                            ccAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGt        <  1:1376299/71‑1 (MQ=255)

                                                            ccAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGt        <  1:2278224/71‑1 (MQ=255)

                                                                 cTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCAccc   >  1:2406211/1‑71 (MQ=255)

                                                                 cTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCAccc   >  1:1918279/1‑71 (MQ=255)

                                                                 cTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCAccc   >  1:1657395/1‑71 (MQ=255)

                                                                  tCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCg  >  1:1299082/1‑71 (MQ=255)

                                                                  tCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCg  >  1:1663129/1‑71 (MQ=255)

GTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCG  >  W3110S.gb/3211610‑3211746

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