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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 385,780 T→C 8.2% F330F (TTT→TTC)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE385,7800TC 8.2% 201.3 / 7.7 74F330F (TTT→TTC) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base T (39/28);  new base C (2/4);  total (42/32)
Fisher's exact test for biased strand distribution p-value = 3.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

TGCCTGCGCTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAA  >  minE/385710‑385845
                                                                      |                                                                 
tGCCTGCGCTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGttt                                                                   <  1:426073/71‑1 (MQ=255)
  ccTGCGCTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTa                                                                  <  1:778557/70‑1 (MQ=255)
  ccTGCGCTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTa                                                                  <  1:3028351/70‑1 (MQ=255)
   cTGCGCTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTAt                                                                 >  1:3533943/1‑70 (MQ=255)
     gcgcTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCa                                                               >  1:810921/1‑70 (MQ=255)
     gcgcTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCAc                                                              >  1:3707196/1‑71 (MQ=255)
      cgcTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCa                                                               <  1:846328/69‑1 (MQ=255)
      cgcTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCAc                                                              >  1:2044381/1‑70 (MQ=255)
       gcTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCa                                                            >  1:1541023/1‑71 (MQ=255)
        cTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCAt                                                           >  1:1362236/1‑71 (MQ=255)
           aCCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCa                                                            >  1:288286/1‑67 (MQ=255)
           aCCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGc                                                        <  1:343799/71‑1 (MQ=255)
           aCCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGc                                                        <  1:755187/71‑1 (MQ=255)
           aCCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGc                                                        >  1:222587/1‑71 (MQ=255)
            ccAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGcc                                                       >  1:1516427/1‑71 (MQ=255)
             cAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCt                                                      >  1:467853/1‑71 (MQ=255)
             cAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCt                                                      >  1:3434150/1‑71 (MQ=255)
                aTTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCtgtg                                                   >  1:3192945/1‑71 (MQ=255)
                   tGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGgc                                                 <  1:2818280/70‑1 (MQ=255)
                     tCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGgcg                                                <  1:3669996/69‑1 (MQ=255)
                       gATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTgg                                                  <  1:3683083/65‑1 (MQ=255)
                       gATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                            >  1:3828734/1‑71 (MQ=255)
                       gATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                            <  1:1263698/71‑1 (MQ=255)
                       gATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                            >  1:1633742/1‑71 (MQ=255)
                        aTGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCAt                                                           >  1:1453569/1‑55 (MQ=255)
                        aTGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCtgtg                                                   >  1:684326/1‑63 (MQ=255)
                        aTGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtg                                           >  1:2924510/1‑71 (MQ=255)
                        aTGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtg                                           <  1:3290708/71‑1 (MQ=255)
                        aTGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgt                                            <  1:1309179/70‑1 (MQ=255)
                         tGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtgt                                          <  1:3877747/71‑1 (MQ=255)
                         tGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtgt                                          >  1:1491976/1‑71 (MQ=255)
                         tGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtg                                           >  1:1409432/1‑70 (MQ=255)
                          ggCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGgtgt                                          <  1:2279203/70‑1 (MQ=255)
                          ggCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTc                                         >  1:3515144/1‑71 (MQ=255)
                           gCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCt                                        <  1:2956593/71‑1 (MQ=255)
                              cTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCa                                                               <  1:1716627/45‑1 (MQ=255)
                              cTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                     >  1:3068148/1‑71 (MQ=255)
                              cTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                     <  1:3075591/71‑1 (MQ=255)
                              cTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                     <  1:526407/71‑1 (MQ=255)
                              cTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                     <  1:3521796/71‑1 (MQ=255)
                               tGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCt                                    >  1:404384/1‑71 (MQ=255)
                               tGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCt                                    >  1:2648686/1‑71 (MQ=255)
                               tGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCt                                    >  1:1436778/1‑71 (MQ=255)
                               tGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCAGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGc                                     <  1:503765/70‑1 (MQ=255)
                                ggCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTg                                       >  1:2341011/1‑67 (MQ=255)
                                  cccGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTc                                  >  1:436300/1‑70 (MQ=255)
                                   ccGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCa                                                            >  1:1788500/1‑43 (MQ=255)
                                     ggTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCa                                                               <  1:2970303/38‑1 (MQ=255)
                                     ggTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCAGCATCGCCTGTGGCGCGGTGTCTGGCTTCCATg                              >  1:3508245/1‑71 (MQ=255)
                                         tGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCt                          <  1:1213685/71‑1 (MQ=255)
                                          ggACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCt                          >  1:2096827/1‑70 (MQ=255)
                                           gACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTcc                                 <  1:3007688/62‑1 (MQ=255)
                                            aCCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                       <  1:551934/71‑1 (MQ=255)
                                             ccGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCAt                               >  1:3712824/1‑62 (MQ=255)
                                               ggTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGgcg                                                <  1:1831744/43‑1 (MQ=255)
                                                gTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTgg                                                  >  1:3019949/1‑40 (MQ=255)
                                                 tAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGcgcg                                              <  1:1872008/43‑1 (MQ=255)
                                                 tAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtctt                  <  1:2811760/71‑1 (MQ=255)
                                                  aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                 >  1:589601/1‑71 (MQ=255)
                                                  aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                 >  1:1538696/1‑71 (MQ=255)
                                                  aaCCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCtcttc                 >  1:1879872/1‑71 (MQ=255)
                                                        ttCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAt                       <  1:3291672/59‑1 (MQ=255)
                                                        ttCCCGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCggta            <  1:516376/70‑3 (MQ=255)
                                                         tCCCGTTCATGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGAc           >  1:2241936/1‑70 (MQ=255)
                                                           ccGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAcga         <  1:2624561/70‑3 (MQ=255)
                                                           ccGTTCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAcga         <  1:198973/70‑3 (MQ=255)
                                                            cGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCAc        >  1:3610705/1‑70 (MQ=255)
                                                            cGTTCCTGTTGATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTacgacg       >  1:3111843/1‑71 (MQ=255)
                                                              ttCCTGTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCa                                >  1:3835678/1‑44 (MQ=38)
                                                                ccTGTTTATCACCATCGCCTGTGGCGCGGTGTCTg                                       >  1:2384902/1‑35 (MQ=255)
                                                                 cTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCAGGCCGaa  <  1:513094/71‑1 (MQ=255)
                                                                   gTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGAtctc                    >  1:2085774/1‑51 (MQ=255)
                                                                   gTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCg    >  1:871837/1‑67 (MQ=255)
                                                                   gTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCac                               >  1:1267480/1‑39 (MQ=37)
                                                                   gTTCATCACCATCGCCTGTGGTGCGGTATCTGGCTTCCACGCGCTGATCTCTTCCGGTAcga         <  1:345865/62‑3 (MQ=255)
                                                                    tttATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATgca                            >  1:2946110/1‑41 (MQ=255)
                                                                      |                                                                 
TGCCTGCGCTGACCAAATTTGTCGATGGCACTGGCCCGGTATGGACCGGTAACCTGTTCCCGTTCCTGTTTATCACCATCGCCTGTGGCGCGGTGTCTGGCTTCCATGCGCTGATCTCTTCTGGGACCACGCCGAA  >  minE/385710‑385845

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