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	1,230,359	T→A	40.9%	P108P (CCT→CCA)	exoX →	DNA exonuclease X

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,230,359	0	T	A	40.9%	28.8 / 63.8	66	P108P (CCT→CCA)	exoX	DNA exonuclease X
Reads supporting (aligned to +/- strand): ref base T (17/22); new base A (23/4); total (40/26)
Fisher's exact test for biased strand distribution p-value = 8.10e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.92e-01

CTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAGCTC  >  minE/1230300‑1230404

cTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAg                                      >  1:3212874/1‑69 (MQ=255)

cTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAg                                      >  1:2743194/1‑69 (MQ=255)

cTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAg                                      >  1:1835198/1‑69 (MQ=255)

cTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAg                                      >  1:1594834/1‑69 (MQ=255)

cTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAg                                      >  1:1768055/1‑69 (MQ=255)

  gCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGt                                     <  1:903755/68‑1 (MQ=255)

  gCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGt                                     <  1:3119247/68‑1 (MQ=255)

  gCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGt                                     <  1:2135719/68‑1 (MQ=255)

  gCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGt                                     <  1:1993135/68‑1 (MQ=255)

  gCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGt                                     <  1:1682007/68‑1 (MQ=255)

     tGAAATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAg                                 <  1:1029839/69‑1 (MQ=255)

     tGAAATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAg                                 <  1:3016323/69‑1 (MQ=255)

     tGAAATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAg                                 <  1:609177/69‑1 (MQ=255)

     tGAAATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAg                                 <  1:1806195/69‑1 (MQ=255)

         aTGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              <  1:71633/68‑1 (MQ=255)

         aTGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              <  1:2669540/68‑1 (MQ=255)

         aTGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              <  1:278691/68‑1 (MQ=255)

         aTGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              <  1:1902739/68‑1 (MQ=255)

                gTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              <  1:2550477/61‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              >  1:1184920/1‑54 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              >  1:2440433/1‑54 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              >  1:341473/1‑54 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:1475460/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:3385238/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:2563976/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:2752886/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:2284692/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:628703/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:1207236/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:1537445/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:3199924/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGc                        <  1:3185794/60‑1 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATaa               >  1:2315667/1‑69 (MQ=255)

                       gATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATaa               >  1:2536704/1‑69 (MQ=255)

                           tGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAaca           >  1:1597461/1‑69 (MQ=255)

                           tGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAaca           >  1:2625545/1‑69 (MQ=255)

                            gCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCaa                              <  1:373924/49‑1 (MQ=255)

                                 aTGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAg     >  1:2648657/1‑69 (MQ=255)

                                 aTGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAg     <  1:2723246/69‑1 (MQ=255)

                                 aTGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAg     >  1:2891135/1‑69 (MQ=255)

                                 aTGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAg     >  1:433688/1‑69 (MQ=255)

                                 aTGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAg     >  1:3104556/1‑69 (MQ=255)

                                 aTGAAACTGGCCCGCCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAg     >  1:1676476/1‑69 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGc    >  1:850776/1‑65 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:3392498/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:3376346/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:707928/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:693022/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1039747/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2001386/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1145826/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1249125/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1289026/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:141255/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1502740/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1836711/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2971956/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:232515/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2372133/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2754187/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2879037/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2899232/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:2902513/1‑66 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCTc  >  1:2592380/1‑67 (MQ=255)

                                      aCTGGCCCGTCGTTTGTGGCCAGGGATCAAGTACAG‑AATATGGCGCTATATAAAACACGGAAGCt   >  1:1800958/1‑65 (MQ=255)

                                      aCTGGCACGTCGTTTGTGGCCAGGGATCAAGTACAGCAATATGGCGCTATATAAAACACGGAAGCt   >  1:1895315/1‑66 (MQ=255)

CTGCCTGAGATGCCCGGTGAGTGGATTTGCACTATGAAACTGGCCCGTCGTTTGTGGCCTGGGATCAAGTACAGCAATATGGCGTTATATAAAACACGCAAGCTC  >  minE/1230300‑1230404

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