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 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,135,734	A→G	28.7%	D199D (GAT→GAC)	pnp ←	polynucleotide phosphorylase/polyadenylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,135,734	0	A	G	28.7%	55.9 / 24.3	59	D199D (GAT→GAC)	pnp	polynucleotide phosphorylase/polyadenylase
Reads supporting (aligned to +/- strand): ref base A (24/18); new base G (14/3); total (38/21)
Fisher's exact test for biased strand distribution p-value = 8.00e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTA  >  minE/2135682‑2135796

gAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGctctct                                                 >  1:1549850/1‑68 (MQ=255)

      cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                                          >  1:1056027/1‑69 (MQ=255)

      cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                                          >  1:3323665/1‑69 (MQ=255)

      cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                                          >  1:3149275/1‑69 (MQ=255)

      cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                                          >  1:2439493/1‑69 (MQ=255)

      cAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCt                                          >  1:606833/1‑69 (MQ=255)

      cAGATTCAACCATCAGCGCGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:3412704/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:386978/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:1480017/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:1533707/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:733553/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:3053334/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:959368/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:1221387/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:1869535/1‑67 (MQ=255)

      cAGATTCAACCATCAGCACGGCAGCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAgt                                           >  1:2049678/1‑67 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:2723163/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:1025391/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:584514/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:1200139/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:3085583/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:2089714/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:1927721/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:1683121/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:3280371/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:1601358/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:156297/1‑68 (MQ=255)

           tCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTc                                      >  1:1461641/1‑68 (MQ=255)

                      tACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCggg                            >  1:1402851/1‑67 (MQ=255)

                      tACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCggg                            >  1:2489553/1‑67 (MQ=255)

                      tACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGATTGCTCTCTTTCAGCTCGTCCTGAGTCgg                             >  1:2985779/1‑66 (MQ=255)

                       aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         <  1:353479/69‑1 (MQ=255)

                       aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         <  1:509243/69‑1 (MQ=255)

                       aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         <  1:1380444/69‑1 (MQ=255)

                       aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         <  1:2602134/69‑1 (MQ=255)

                       aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         <  1:2510639/69‑1 (MQ=255)

                       aCAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         <  1:2133808/69‑1 (MQ=255)

                        cAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGtt                          >  1:609463/1‑67 (MQ=255)

                        cAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         >  1:2996831/1‑68 (MQ=255)

                        cAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTc                         >  1:2253520/1‑68 (MQ=255)

                          gcagCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAg                       <  1:2853806/65‑1 (MQ=255)

                          gcagCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAg                       <  1:1610732/65‑1 (MQ=255)

                           cagCTTCTGTACCCGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAg                       <  1:1189672/65‑1 (MQ=255)

                            agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCg                              >  1:247428/2‑59 (MQ=255)

                            agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAgta                     >  1:639637/2‑68 (MQ=255)

                            agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAgta                     >  1:2486931/2‑68 (MQ=255)

                            agCTTCTGTACCGGCAACAACCAGGTCCAGTTTGCTCTCTTTCAGTTCGTCCTGAGTCGGGTTCAgta                     >  1:2452657/2‑68 (MQ=255)

                             gCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacg                   <  1:1070261/69‑1 (MQ=255)

                             gCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacg                   <  1:998097/69‑1 (MQ=255)

                              cTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacgt                  <  1:1347906/69‑1 (MQ=255)

                              cTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacgt                  <  1:978676/69‑1 (MQ=255)

                                             caacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAgtacgt                  <  1:535915/54‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:3381566/69‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:3001081/69‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:2905116/69‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:1655022/69‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:1625837/69‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:680677/69‑1 (MQ=255)

                                              aacCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTa  <  1:1284892/69‑1 (MQ=255)

GAGCTTCAGATTCAACCATCAGTACAGCGGCTTCAGTACCGGCAACAACCAGATCCAGTTTGCTCTCTTTCAGCTCGTCCTGAGTCGGGTTCAGTACGTACTGGTCATTGATGTA  >  minE/2135682‑2135796

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