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 F1 I2 R1	772	77.0	3769570	91.6%	3452926	105.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,764,759	G→A	P132L (CCA→CTA)	yfjL ←	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,764,759	0	G	A	98.4%	198.8 / NA	62	P132L (CCA→CTA)	yfjL	CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (32/29); minor base C (1/0); total (33/29)
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

TAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTGGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCATTGATTTGTGCAAAATTGAA  >  NC_000913/2764623‑2764893

tAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGc                                                                                                                                      >  2:1663948/1‑139 (MQ=255)

 aGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCt                                                                                                                                     >  1:1445295/1‑139 (MQ=255)

        ccAGTTCGCGCAGGGATGAAAACACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAg                                                                                                                              >  2:950902/1‑139 (MQ=255)

        ccAGTTCGCGCAGGGATGAAAACACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAg                                                                                                                              >  2:78764/1‑139 (MQ=255)

                           aaaCACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATc                                                                                                           <  2:1445295/139‑1 (MQ=255)

                                  tCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGt                                                                                                    >  2:1059277/1‑139 (MQ=255)

                                      aTGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTc                                                                                                >  1:239633/1‑139 (MQ=255)

                                           gCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGCGTTCCTGTCGCCCTCGCTTATCTAGTCGGGCGTTTGGTCTGATCGTCAAGTACTCAAggg                                                                                           >  1:467182/1‑139 (MQ=255)

                                           gCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAggg                                                                                           >  2:1184532/1‑139 (MQ=255)

                                                 tCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTttgt                                                                                     <  1:1184532/139‑1 (MQ=255)

                                                 tCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTttgt                                                                                     <  2:42846/139‑1 (MQ=255)

                                                 tCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTttgt                                                                                     <  1:993125/139‑1 (MQ=255)

                                                     tCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGa                                                                                                             >  1:1320703/1‑111 (MQ=255)

                                                     tCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGa                                                                                                             <  2:1320703/111‑1 (MQ=255)

                                                                 cGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCtgt                                                                     <  1:1663948/139‑1 (MQ=255)

                                                                    ttATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGa                                                                                                             <  2:1711552/96‑1 (MQ=255)

                                                                    ttATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGa                                                                                                             >  1:1711552/1‑96 (MQ=255)

                                                                    ttATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGAc                                                                  <  1:1615466/139‑1 (MQ=255)

                                                                     tataCCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTAAAGGGTTATGTTGACCTTTTCCTCTGTGACg                                                                 <  2:467182/139‑1 (MQ=255)

                                                                      ataCCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGa                                                                >  1:335339/1‑139 (MQ=255)

                                                                      ataCCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGa                                                                <  1:78764/139‑1 (MQ=255)

                                                                          cTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGa                                                            <  1:1059277/139‑1 (MQ=255)

                                                                             aGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGACCGTc                                                                                                        >  2:569554/1‑92 (MQ=255)

                                                                             aGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGACCGTc                                                                                                        <  1:569554/92‑1 (MQ=255)

                                                                                cTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTg                                                                                                              <  1:1324808/83‑1 (MQ=255)

                                                                                cTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTg                                                                                                              >  2:1324808/1‑83 (MQ=255)

                                                                                 tGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGa                                                                <  2:1615760/128‑1 (MQ=255)

                                                                                 tGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGa                                                                >  1:1615760/1‑128 (MQ=255)

                                                                                 tGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTa                                                     >  1:806025/1‑139 (MQ=255)

                                                                                  gTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTAc                                                    >  2:591604/1‑139 (MQ=255)

                                                                                  gTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTAc                                                    >  1:1016904/1‑139 (MQ=255)

                                                                                   ttAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAggg                                                                                           >  2:1432527/1‑99 (MQ=255)

                                                                                   ttAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAggg                                                                                           <  1:1432527/99‑1 (MQ=255)

                                                                                           ttgagtgtgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGTAGTACCTACGTCCAAggt                                           >  1:30019/6‑138 (MQ=255)

                                                                                             gTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGAc                                         <  1:950902/139‑1 (MQ=255)

                                                                                                tgtgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGc                                                                                                                >  2:880363/1‑65 (MQ=255)

                                                                                                tgtgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGc                                                                                                                <  1:880363/65‑1 (MQ=255)

                                                                                                  tgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCggg                                                                                                                         >  1:943158/1‑54 (MQ=255)

                                                                                                  tgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCggg                                                                                                                         <  2:943158/54‑1 (MQ=255)

                                                                                                  tgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACt                                                                                                 <  1:1819438/78‑1 (MQ=255)

                                                                                                  tgCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACt                                                                                                 >  2:1819438/1‑78 (MQ=255)

                                                                                                        tgttgAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTc                              >  1:319805/1‑139 (MQ=255)

                                                                                                           tgAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTcaca                           <  2:139464/139‑1 (MQ=255)

                                                                                                           tgAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTcaca                           <  2:335339/139‑1 (MQ=255)

                                                                                                            gAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATc                                                                                                           <  2:189332/58‑1 (MQ=255)

                                                                                                            gAGGTCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATc                                                                                                           >  1:189332/1‑58 (MQ=255)

                                                                                                                tCATCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCa                      <  2:806025/139‑1 (MQ=255)

                                                                                                                  aTCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCAtt                    >  1:18643/1‑139 (MQ=255)

                                                                                                                   tCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTcaca                           <  1:1731971/131‑1 (MQ=255)

                                                                                                                   tCGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTcaca                           >  2:1731971/1‑131 (MQ=255)

                                                                                                                    cGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACg                                                                 <  1:1405698/92‑1 (MQ=255)

                                                                                                                    cGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACg                                                                 >  2:1405698/1‑92 (MQ=255)

                                                                                                                    cGATGAGTTCCTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCATTGa                  >  2:63848/1‑139 (MQ=255)

                                                                                                                             ccTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGc                                                                                                                >  2:1047879/1‑36 (MQ=255)

                                                                                                                             ccTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGc                                                                                                                <  1:1047879/36‑1 (MQ=255)

                                                                                                                              cTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTcaca                           <  2:1250219/120‑1 (MQ=255)

                                                                                                                              cTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTcaca                           >  1:1250219/1‑120 (MQ=255)

                                                                                                                              cTGTCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCATTGATTTGTGCaaa        >  2:1870845/1‑139 (MQ=255)

                                                                                                                                 tCGACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCATTGATTTGTGCAAAAtt     >  2:1399036/1‑139 (MQ=255)

                                                                                                                                   gACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTttgt                                                                                     <  2:212049/57‑1 (MQ=255)

                                                                                                                                   gACCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTttgt                                                                                     >  1:212049/1‑57 (MQ=255)

                                                                                                                                    aCCTAGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCATTGATTTGTGCAAAATTGaa  <  2:18643/139‑1 (MQ=255)

TAGAAGTTCCAGTTCGCGCAGGGATGAAAACACTTCCCATGTAGCCGCATCGATCCAATCTGAAACGCTTATACCTGAGTCTGTTAAAAAATTGTCTGTGCGTTTGTTGAGGTCATCGATGAGTTCCTGTCGACCTGGCTTATCTAGTCGGGCGTTTGGGCTGATCGTCAAGTACTCAAGGGTTTTGTTGACCTTTTCCTCTGTGACGATGGAGTACCTACGTCCAAGGGACAGGTCAGACTCACACTGCATTGATTTGTGCAAAATTGAA  >  NC_000913/2764623‑2764893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A