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 F3 I0 R2	232	76.3	4135488	90.9%	3759158	60.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,971,396	T→C	35.9%	V71A (GTG→GCG)	serB →	3‑phosphoserine phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,971,396	0	T	C	35.9%	56.7 / 66.9	64	V71A (GTG→GCG)	serB	3‑phosphoserine phosphatase
Reads supporting (aligned to +/- strand): ref base T (12/29); new base C (13/10); total (25/39)
Fisher's exact test for biased strand distribution p-value = 3.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.55e-01

AAACAACGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGCCTGGCCCACGAAGCG  >  minE/2971329‑2971466

aaaCAACGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTgg                                                                      >  1:814161/1‑70 (MQ=255)

     acGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGAt                                                                 >  1:2258598/1‑70 (MQ=255)

     acGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGAt                                                                 >  1:3505639/1‑70 (MQ=255)

     acGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGAt                                                                 >  1:345521/1‑70 (MQ=255)

     acGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGAt                                                                 >  1:1627004/1‑70 (MQ=255)

      cGTCTGAGCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTa                                                               >  1:2088382/1‑71 (MQ=255)

      cGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGAtt                                                                <  1:2960580/70‑1 (MQ=255)

      cGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTa                                                               >  1:3504321/1‑71 (MQ=255)

          tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGTTTGTTGCCGCCTGGTGCGTGGAAGATTATCAg                                                           >  1:3552608/1‑71 (MQ=255)

          tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAg                                                           >  1:3773386/1‑71 (MQ=255)

          tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAg                                                           >  1:463919/1‑71 (MQ=255)

            aCCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGt                                                         <  1:3942144/71‑1 (MQ=255)

            aCCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGt                                                         <  1:2521330/71‑1 (MQ=255)

            aCCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAg                                                           <  1:3432823/69‑1 (MQ=255)

            aCCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAg                                                           <  1:1277517/69‑1 (MQ=255)

            aCCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGt                                                         <  1:2402624/71‑1 (MQ=255)

            aCCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGt                                                         <  1:3505959/71‑1 (MQ=255)

             cccAATACCAGAGCAAACTGGGTGCTGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTg                                                        <  1:1332728/71‑1 (MQ=255)

             cccAATACCAGAGCAAACTGGGTGCTGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTg                                                        <  1:1327919/71‑1 (MQ=255)

             cccAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGt                                                         <  1:2419557/70‑1 (MQ=255)

             cccAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAg                                                           <  1:292932/68‑1 (MQ=255)

              ccAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGa                                                       <  1:4063733/71‑1 (MQ=255)

                  tACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCg                                                   <  1:1275172/71‑1 (MQ=255)

                  tACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCg                                                   >  1:1955792/1‑71 (MQ=255)

                  tACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCg                                                   >  1:3096807/1‑71 (MQ=255)

                  tACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCg                                                   >  1:2363449/1‑71 (MQ=255)

                  tACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCg                                                   >  1:1901561/1‑71 (MQ=255)

                  tACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCg                                                   >  1:3574773/1‑71 (MQ=255)

                   aCCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGaa                                                                    <  1:2254901/53‑1 (MQ=255)

                    ccAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTg                                                        <  1:3241217/64‑1 (MQ=255)

                        agCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGc                                             <  1:2393628/71‑1 (MQ=255)

                          cAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCa                                                            <  1:867063/54‑1 (MQ=255)

                          cAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCa                                                            <  1:2679373/54‑1 (MQ=255)

                           aaaCTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCa                                                            <  1:887598/53‑1 (MQ=255)

                            aaCTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTa                                                               <  1:3328549/49‑1 (MQ=255)

                            aaCTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTa                                                               <  1:4027222/49‑1 (MQ=255)

                            aaCTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTc                                                    <  1:3163218/60‑1 (MQ=255)

                              cTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGAt                                                                 <  1:3872122/45‑1 (MQ=255)

                               tGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGAt                                                                 <  1:622587/44‑1 (MQ=255)

                                      ggcgATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCg                               <  1:2431510/71‑1 (MQ=255)

                                      ggcgATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCg                               <  1:1245419/71‑1 (MQ=255)

                                      ggcgATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCg                               <  1:1226592/71‑1 (MQ=255)

                                             gTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTtcactca                                  >  1:2670122/1‑61 (MQ=255)

                                              tGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGAt                                                      <  1:3125622/40‑1 (MQ=255)

                                              tGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGAt                                                      <  1:3136165/40‑1 (MQ=255)

                                              tGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGAt                                                      <  1:2212623/40‑1 (MQ=255)

                                              tGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACggg                         >  1:347160/1‑69 (MQ=255)

                                              tGATTGTTGCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGc                        >  1:2596687/1‑70 (MQ=255)

                                                agtgttgCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      <  1:932995/68‑1 (MQ=255)

                                                aTTGTTGCCGCCTTGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      <  1:3726389/70‑1 (MQ=255)

                                                aTTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      <  1:2366928/70‑1 (MQ=255)

                                                aTTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      >  1:1458860/1‑70 (MQ=255)

                                                aTTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      <  1:779040/70‑1 (MQ=255)

                                                aTTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      <  1:1211923/70‑1 (MQ=255)

                                                aTTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTa                      <  1:1018422/70‑1 (MQ=255)

                                                aTTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGCCTa                      <  1:1870559/70‑1 (MQ=255)

                                                  tgttgCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTacac                   >  1:2327315/1‑71 (MQ=255)

                                                  tgttgCCGCCTGGTGCGCGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTacac                   >  1:1388559/1‑71 (MQ=255)

                                                    ttgCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGc                 >  1:3949079/1‑71 (MQ=255)

                                                    ttgCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGc                 >  1:4049001/1‑71 (MQ=255)

                                                            tGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGCCTGGCCCa         >  1:2388827/1‑71 (MQ=255)

                                                            tGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGCCTGGCCCa         >  1:87696/1‑71 (MQ=255)

                                                            tGGTGCGCGGAAGATTATCAGGTGATTCGTCTGGCAGGTtca                                      <  1:1345590/42‑1 (MQ=255)

                                                            tGGTGCGCGGAAGATTATCAGGTGATTCGTCTGGCAGGTtca                                      <  1:1276437/42‑1 (MQ=255)

                                                                   tGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGCCTGGCCCACGAAgcg  >  1:3042363/1‑71 (MQ=255)

AAACAACGTCTGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATTCGTCTGGCAGGTTCACTCACCGCACGGGCTACACGCCTGGCCCACGAAGCG  >  minE/2971329‑2971466

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